View Filing Data

Document and Entity Information - USD ($) $ in Millions	12 Months Ended
Document and Entity Information - USD ($) $ in Millions	Dec. 31, 2018	Mar. 01, 2019	Jun. 29, 2018
Document And Entity Information [Abstract]
Document Type	10-K
Amendment Flag	false
Document Period End Date	Dec. 31, 2018
Document Fiscal Year Focus	2018
Document Fiscal Period Focus	FY
Trading Symbol	ZFGN
Entity Registrant Name	ZAFGEN, INC.
Entity Central Index Key	0001374690
Current Fiscal Year End Date	--12-31
Entity Well-known Seasoned Issuer	No
Entity Current Reporting Status	Yes
Entity Voluntary Filers	No
Entity Filer Category	Accelerated Filer
Entity Small Business	true
Entity Emerging Growth Company	true
Entity Ex Transition Period	true
Entity Shell Company	false
Entity Common Stock, Shares Outstanding		37,315,118
Entity Public Float			$ 201.8

Consolidated Balance Sheets - USD ($) $ in Thousands	Dec. 31, 2018	Dec. 31, 2017
Current assets:
Cash and cash equivalents	$ 49,331	$ 40,777
Marketable securities	68,735	61,275
Tax incentive receivable	1,536	946
Prepaid expenses and other current assets	1,728	1,927
Total current assets	121,330	104,925
Property and equipment, net	375	528
Other assets	57	57
Total assets	121,762	105,510
Current liabilities:
Accounts payable	3,590	3,020
Accrued expenses	4,261	4,273
Notes payable, current	5,455
Total current liabilities	13,306	7,293
Notes payable, long-term	15,185	20,000
Total liabilities	28,491	27,293
Commitments and contingencies (Note 10)
Stockholders' equity:
Preferred stock; $0.001 par value per share; 5,000,000 shares authorized as of December 31, 2018 and 2017; no shares issued and outstanding as of and December 31, 2018 and 2017
Common stock, $0.001 par value per share; 115,000,000 shares authorized as of December 31, 2018 and 2017; 37,287,221 and 27,489,457 shares issued and outstanding as of December 31, 2018 and 2017, respectively	37	27
Additional paid-in capital	444,212	367,825
Accumulated deficit	(350,945)	(289,577)
Accumulated other comprehensive loss	(33)	(58)
Total stockholders' equity	93,271	78,217
Total liabilities and stockholders' equity	$ 121,762	$ 105,510

Consolidated Balance Sheets (Parenthetical) - $ / shares	Dec. 31, 2018	Dec. 31, 2017
Statement Of Financial Position [Abstract]
Preferred stock, par value per share	$ 0.001	$ 0.001
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value per share	$ 0.001	$ 0.001
Common stock, shares authorized	115,000,000	115,000,000
Common stock, shares issued	37,287,221	27,489,457
Common stock, shares outstanding	37,287,221	27,489,457

Consolidated Statements of Operations and Comprehensive Loss - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Income Statement [Abstract]
Revenue	$ 0	$ 0	$ 0
Operating expenses:
Research and development	47,929	40,839	39,936
General and administrative	13,193	12,160	18,289
Total operating expenses	61,122	52,999	58,225
Loss from operations	(61,122)	(52,999)	(58,225)
Other income (expense):
Interest income	1,889	996	894
Interest expense	(1,898)	(165)	(529)
Foreign currency transaction (losses) gains, net	(237)	140	(18)
Total other (expense) income, net	(246)	971	347
Net loss	$ (61,368)	$ (52,028)	$ (57,878)
Net loss per share, basic and diluted	$ (1.90)	$ (1.90)	$ (2.12)
Weighted average common shares outstanding, basic and diluted	32,228,721	27,433,239	27,297,934
Comprehensive loss:
Net loss	$ (61,368)	$ (52,028)	$ (57,878)
Other comprehensive loss:
Unrealized gain on marketable securities	25	22	127
Total other comprehensive gain	25	22	127
Total comprehensive loss	$ (61,343)	$ (52,006)	$ (57,751)

Consolidated Statements of Changes in Stockholders' Equity - USD ($) $ in Thousands	Total	Common Stock [Member]	Additional Paid-in Capital [Member]	Accumulated Deficit [Member]	Accumulated Other Comprehensive Loss [Member]
Beginning balance at Dec. 31, 2015	$ 169,110	$ 27	$ 348,961	$ (179,671)	$ (207)
Beginning balance, shares at Dec. 31, 2015		27,242,503
Issuance of common stock upon exercise of stock options and employee stock purchase plan	220		220
Issuance of common stock upon exercise of stock options and employee stock purchase plan, shares		72,663
Issuance of common stock, net of issuance costs	35		35
Issuance of common stock, net of issuance costs, shares		5,564
Issuance of restricted stock units, shares		11,821
Stock-based compensation expense	10,113		10,113
Unrealized gain on marketable securities	127				127
Net loss	(57,878)			(57,878)
Ending balance at Dec. 31, 2016	121,727	$ 27	359,329	(237,549)	(80)
Ending balance, shares at Dec. 31, 2016		27,332,551
Issuance of common stock upon exercise of stock options and employee stock purchase plan	195		195
Issuance of common stock upon exercise of stock options and employee stock purchase plan, shares		136,992
Issuance of restricted stock units, shares		19,914
Stock-based compensation expense	8,301		8,301
Unrealized gain on marketable securities	22				22
Net loss	(52,028)			(52,028)
Ending balance at Dec. 31, 2017	78,217	$ 27	367,825	(289,577)	(58)
Ending balance, shares at Dec. 31, 2017		27,489,457
Issuance of common stock upon exercise of stock options and employee stock purchase plan	2,360	$ 1	2,359
Issuance of common stock upon exercise of stock options and employee stock purchase plan, shares		578,842
Issuance of common stock, net of issuance costs	64,410	$ 9	64,401
Issuance of common stock, net of issuance costs, shares		9,200,000
Issuance of restricted stock units, shares		18,922
Stock-based compensation expense	9,627		9,627
Unrealized gain on marketable securities	25				25
Net loss	(61,368)			(61,368)
Ending balance at Dec. 31, 2018	$ 93,271	$ 37	$ 444,212	$ (350,945)	$ (33)
Ending balance, shares at Dec. 31, 2018		37,287,221

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Cash flows from operating activities:
Net loss	$ (61,368)	$ (52,028)	$ (57,878)
Adjustments to reconcile net loss to net cash used in operating activities:
Stock-based compensation expense	9,627	8,301	10,113
Non-cash interest expense		13	43
Depreciation expense	261	188	212
Loss on disposal of research and development equipment			328
Unrealized foreign currency transaction losses (gains)	76	(46)	6
Premium on marketable securities, net	(6)	(359)	(340)
Amortization of (discount) premium on marketable securities	(670)	246	1,037
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	199	(569)	413
Tax incentive receivable	(666)	(553)	970
Accounts payable	432	448	(4,625)
Accrued expenses	628	575	(2,254)
Net cash used in operating activities	(51,487)	(43,784)	(51,975)
Cash flows from investing activities:
Proceeds from sales and maturities of marketable securities	110,388	150,213	188,600
Purchases of marketable securities	(117,147)	(114,511)	(136,528)
Purchases of property and equipment	(108)	(55)	(660)
Deposits for leased property			35
Net cash (used in) provided by investing activities	(6,867)	35,647	51,447
Cash flows from financing activities:
Proceeds from issuance of notes payable		20,000
Repayments of notes payable		(3,633)	(2,935)
Proceeds from exercise of common stock options and employee stock purchase plan	2,360	195	220
Proceeds from public offerings, net of commissions and underwriting discounts	64,860
Payments of public offering costs	(312)
Net cash provided by (used in) financing activities	66,908	16,562	(2,715)
Net increase (decrease) in cash and cash equivalents	8,554	8,425	(3,243)
Cash and cash equivalents at beginning of period	40,777	32,352	35,595
Cash and cash equivalents at end of period	49,331	40,777	32,352
Supplemental disclosure of non-cash investing and financing activities:
Public offering costs included in accounts payable	138
Supplemental disclosure of cash flow information:
Cash paid for interest	$ 1,144	$ 141	$ 388

Nature of the Business and Basis of Presentation

12 Months Ended

Dec. 31, 2018

Accounting Policies [Abstract]

Nature of the Business and Basis of Presentation

1. Nature of the Business and Basis of Presentation

Zafgen, Inc., or the Company, was incorporated on November 22, 2005 under the laws of the State of Delaware. The Company is a clinical-stage biopharmaceutical company leveraging its proprietary knowledge of the methionine aminopeptidase 2 (“MetAP2”) pathway to develop novel therapies for patients affected by a range of complex metabolic diseases. Zafgen has pioneered the study of MetAP2 inhibitors in both common and rare metabolic disorders, and its current disease areas of focus are type 2 diabetes, Prader-Willi syndrome (“PWS”) and liver diseases. The Company’s lead product candidate is ZGN-1061, a MetAP2 inhibitor in Phase 2 clinical development with unique properties that maximize impact on metabolic parameters relevant to the treatment of type 2 diabetes and other related metabolic disorders. In January 2018, the Company announced advancement of its highly optimized MetAP2 development candidate ZGN-1258, and in the first quarter of 2018, initiated investigational new drug application (“IND”) enabling nonclinical efforts for evaluation in the treatment of people affected by PWS. In March 2019, we announced our decision to suspend plans to file an IND for ZGN-1258 in order to evaluate ZGN-1258 following an unexpected finding in muscle tissue in rodent toxicology studies. During the fourth quarter of 2018 the Company announced that ZGN-1345, an orally dosed MetAP2 inhibitor specifically targeting the liver, has been formally advanced to development candidate stage. The Company is subject to risks common to companies in the biotechnology industry including, but not limited to, new technological innovations, protection of proprietary technology, dependence on key personnel, compliance with government regulations and the need to obtain additional financing. Product candidates currently under development will require significant additional research and development efforts, including extensive nonclinical and clinical testing and regulatory approval, prior to commercialization. These efforts require significant amounts of additional capital, adequate personnel infrastructure, and extensive compliance-reporting capabilities.

The Company’s product candidates are all in the research and development stage. There can be no assurance that the Company’s research and development will be successfully completed, that adequate protection for the Company’s intellectual property will be obtained, that any product candidates developed will obtain necessary government regulatory approval or that any approved products will be commercially viable. Even if the Company’s product development efforts are successful, it is uncertain when, if ever, the Company will generate significant revenue from product sales. The Company operates in an environment of rapid change in technology and substantial competition from pharmaceutical and biotechnology companies. In addition, the Company is dependent upon the services of its employees and consultants.

The Company has incurred losses and negative cash flows from operations since its inception. As of December 31, 2018, the Company had an accumulated deficit of $350.9 million. From its inception through December 31, 2018, the Company received net proceeds of $397.9 million from the sales of redeemable convertible preferred stock, the issuance of convertible promissory notes, the proceeds from its initial public offering (“IPO”) in June 2014 and its follow-on offerings in January 2015 and July 2018. On July 2, 2018, the Company completed a public offering of its common stock, which resulted in the sale of 9,200,000 shares at a price of $7.50 per share, resulting in net proceeds of approximately $64.6 million after deducting underwriting discounts and commissions, as well as offering costs. As disclosed in Note 6 to the consolidated financial statements, the Company has a term loan with an aggregate principal balance of $20.0 million as of December 31, 2018. The loan agreement requires that the Company maintain certain minimum liquidity at all times, which as of December 31, 2018, was approximately $21.0 million. If the minimum liquidity covenant is not met, the Company may be required to repay the loans prior to scheduled maturity dates. Until such time, if ever, as the Company can generate substantial product revenue, the Company expects to finance its cash needs through a combination of equity offerings, debt financings, collaborations, strategic alliances, licensing arrangements and other sources of funding.

Based on its current operating plans, the Company believes its cash, cash equivalents and marketable securities of $118.1 million as of December 31, 2018 will be sufficient to fund its anticipated level of operations, capital expenditures and satisfy debt repayments for a period of at least 12 months from the issuance date of this Annual Report. The Company expects to generate operating losses for the foreseeable future. If the Company is unable to raise additional funds through equity or debt financings, the Company may be required to delay, limit, reduce or terminate product development or future commercialization efforts or grant rights to develop and market products or product candidates that the Company would otherwise prefer to develop and market itself.

The consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries Zafgen Securities Corporation, Zafgen Australia Pty Limited, and Zafgen Animal Health, LLC. All intercompany balances and transactions have been eliminated.

The accompanying consolidated financial statements have been prepared in conformity with accounting principles generally accepted in the United States of America (“GAAP”).

Summary of Significant Accounting Policies

12 Months Ended

Dec. 31, 2018

Accounting Policies [Abstract]

Summary of Significant Accounting Policies

2. Summary of Significant Accounting Policies

Use of Estimates

The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities as of the date of the consolidated financial statements, and the reported amounts of expenses during the reporting periods. Significant estimates and assumptions reflected in these consolidated financial statements include, but are not limited to, the accrual of research and development expenses and the valuation of stock-based awards. Estimates are periodically reviewed in light of changes in circumstances, facts and experience. Actual results could differ from the Company’s estimates.

Cash Equivalents

The Company considers all short-term, highly liquid investments with original maturities of ninety days or less at acquisition date to be cash equivalents. Cash equivalents, which consist of money market funds, U.S. government securities, corporate bonds, and commercial paper, are stated at fair value.

Concentration of Credit Risk and of Significant Suppliers

Financial instruments that potentially expose the Company to concentrations of credit risk consist primarily of cash, cash equivalents and marketable securities. The Company has all cash, cash equivalents and marketable securities balances at three accredited financial institutions in amounts that exceed federally insured limits. The Company does not believe that it is subject to unusual credit risk beyond the normal credit risk associated with commercial banking relationships.

The Company is dependent on third-party manufacturers to supply products for research and development activities in its programs. In particular, the Company relies and expects to continue to rely on a small number of manufacturers to supply it with its requirements for the active pharmaceutical ingredients and formulated drugs related to these programs. These programs could be adversely affected by a significant interruption in the supply of active pharmaceutical ingredients and formulated drugs.

Marketable Securities

Marketable securities consist of investments with original maturities greater than ninety days. The Company has classified its investments with maturities beyond one year as short term, based on their highly liquid nature and because such marketable securities represent the investment of cash that is available for current operations. The Company classifies its marketable securities as available-for-sale. Accordingly, these investments are recorded at fair value, which is based on quoted market prices. Unrealized gains and losses are reported as a component of accumulated other comprehensive loss in stockholders’ equity. Realized gains and losses and declines in value judged to be other than temporary are included as a component of other income (expense), net, based on the specific identification method. When determining whether a decline in value is other than temporary, the Company considers various factors, including whether the Company has the intent to sell the security, and whether it is more likely than not that the Company will be required to sell the security prior to recovery of its amortized cost basis. Fair value is determined based on quoted market prices.

Deferred Offering Costs

The Company capitalizes certain legal, accounting and other third-party fees that are directly associated with in-process equity financings as other assets until such financings are consummated. After consummation of the equity financing, these costs are recorded in stockholders’ equity as a reduction of additional paid-in capital generated as a result of the offering or as a reduction to the carrying value of preferred stock issued.

Property and Equipment

Property and equipment are stated at cost less accumulated depreciation. Depreciation expense is recognized using the straight-line method over a three or five-year estimated useful life for equipment, furniture and fixtures and office equipment. Leasehold improvements are amortized over the shorter of the asset life or the term of the lease agreement. Expenditures for repairs and maintenance of assets are charged to expense as incurred. Upon retirement or sale, the cost and related accumulated depreciation of assets disposed of are removed from the accounts and any resulting gain or loss is included in loss from operations.

Impairment of Long-Lived Assets

Long-lived assets consist of property and equipment. Long-lived assets to be held and used are tested for recoverability whenever events or changes in business circumstances indicate that the carrying amount of the assets may not be fully recoverable. Factors that the Company considers in deciding when to perform an impairment review include significant underperformance of the business in relation to expectations, significant negative industry or economic trends, and significant changes or planned changes in the use of the assets. If an impairment review is performed to evaluate a long-lived asset for recoverability, the Company compares forecasts of undiscounted cash flows expected to result from the use and eventual disposition of the long-lived asset to its carrying value. An impairment loss would be recognized when estimated undiscounted future cash flows expected to result from the use of an asset are less than its carrying amount. The impairment loss would be based on the excess of the carrying value of the impaired asset over its fair value, determined based on discounted cash flows. To date, the Company has not recorded any impairment losses on long-lived assets.

Research and Development Costs

Research and development costs are expensed as incurred. Included in research and development expenses are wages, stock-based compensation and benefits of employees, third-party license fees and milestones and other operational costs related to the Company’s research and development activities, including facility-related expenses and external costs of outside vendors engaged to conduct nonclinical studies, manufacturing activities, and clinical trials. The Company records research and development expenses net of any research and development tax incentives the Company is entitled to receive from government authorities.

Research Contract Costs and Accruals

The Company has entered into various research and development contracts with research institutions and other companies both inside and outside of the United States. These agreements are generally cancelable, and related payments are recorded as research and development expenses as incurred. The Company records accruals for estimated ongoing research costs. When evaluating the adequacy of the accrued liabilities, the Company analyzes progress of the studies, including the phase or completion of events, invoices received and contracted costs. Significant judgments and estimates are made in determining the accrued balances at the end of any reporting period. Actual results could differ from the Company’s estimates. The Company’s historical accrual estimates have not been materially different from the actual costs.

Patent Costs

All patent-related costs incurred in connection with filing and prosecuting patent applications are recorded as general and administrative expenses as incurred, as recoverability of such expenditures is uncertain.

Accounting for Stock-Based Compensation

The Company measures all stock-based awards granted to employees and directors based on the fair value on the date of grant using the Black-Scholes option-pricing model. Compensation expense of those awards is recognized over the requisite service period, which is generally the vesting period of the respective award. Typically, the Company issues awards with only service-based and market-based vesting conditions and records the expense for these awards using the straight-line method. The Company accounts for forfeitures as they occur.

For stock-based awards granted to non-employee consultants, compensation expense is recognized over the period during which services are rendered by such consultants until completed. At the end of each financial reporting period prior to completion of the service, the fair value of these awards is re-measured using the then-current fair value of the Company’s common shares and updated assumption inputs in the Black-Scholes option-pricing model.

The Company classifies stock-based compensation expense in its consolidated statements of operations and comprehensive loss in the same manner in which the award recipient’s payroll costs are classified or in which the award recipient’s service payments are classified.

Income Taxes

The Company accounts for income taxes using the asset and liability method, which requires the recognition of deferred tax assets and liabilities for the expected future tax consequences of events that have been recognized in the consolidated financial statements or in the Company’s tax returns. Deferred taxes are determined based on the difference between the financial statement and tax basis of assets and liabilities using enacted tax rates in effect in the years in which the differences are expected to reverse. Changes in deferred tax assets and liabilities are recorded in the provision for income taxes. The Company assesses the likelihood that its deferred tax assets will be recovered from future taxable income and, to the extent it believes, based upon the weight of available evidence, that it is more likely than not that all or a portion of deferred tax assets will not be realized, a valuation allowance is established through a charge to income tax expense. Potential for recovery of deferred tax assets is evaluated by estimating the future taxable profits expected and considering prudent and feasible tax planning strategies.

The Company accounts for uncertainty in income taxes recognized in the consolidated financial statements by applying a two-step process to determine the amount of tax benefit to be recognized. First, the tax position must be evaluated to determine the likelihood that it will be sustained upon external examination by the taxing authorities. If the tax position is deemed more-likely-than-not to be sustained, the tax position is then assessed to determine the amount of benefit to recognize in the consolidated financial statements. The amount of the benefit that may be recognized is the largest amount that has a greater than 50% likelihood of being realized upon ultimate settlement. The provision for income taxes includes the effects of any resulting tax reserves, or unrecognized tax benefits, that are considered appropriate as well as the related net interest and penalties.

Segment Data

The Company manages its operations as a single segment for the purposes of assessing performance and making operating decisions. The Company is a biopharmaceutical company dedicated to significantly improving the health and well-being of patients affected by both rare and prevalent metabolic diseases including type 2 diabetes, PWS, liver diseases and potentially other metabolically related disorders. No revenue has been generated since inception, and all tangible assets are held in the United States.

Comprehensive Loss

Comprehensive loss includes net loss as well as other changes in stockholders’ equity that result from transactions and economic events other than those with stockholders. For the years ended December 31, 2018, 2017 and 2016, the Company’s only element of other comprehensive loss was unrealized gain or (loss) on marketable securities.

Net Loss Per Share

Basic net loss per share is computed by dividing the net loss attributable to common stockholders by the weighted average number of common shares outstanding for the period. Diluted net loss per share attributable to common stockholders is computed by dividing the diluted net loss attributable to common stockholders by the weighted average number of common shares, including potential dilutive common shares assuming the dilutive effect of outstanding stock options and unvested restricted common shares, as determined using the treasury stock method. For periods in which the Company has reported net losses, diluted net loss per common share attributable to common stockholders is the same as basic net loss per common share attributable to common stockholders, since dilutive common shares are not assumed to have been issued if their effect is antidilutive.

Recently Issued and Adopted Accounting Pronouncements

In February 2016, the Financial Accounting Standards Board (the “FASB”) issued ASU No. 2016-02, Leases, and in July 2018, the FASB issued ASU No. 2018-11, Leases (Topic 842): Targeted Improvements. The new leasing standards generally require lessees to recognize operating and financing lease liabilities and corresponding right-of-use assets on the consolidated balance sheet and to provide enhanced disclosures surrounding the amount, timing and uncertainty of cash flows arising from leasing arrangements. The Company will adopt the new standard effective January 1, 2019 and will not restate comparative periods. Presentation of leases within the consolidated statements of operations and comprehensive loss and consolidated statements of cash flows will be generally consistent with the current lease accounting guidance. The Company will elect the package of practical expedients permitted under the transition guidance and as such, the adoption of this ASU will not change the classification of any of the Company’s leases. The Company will elect to combine lease and non-lease components, elect not to record leases with an initial term of 12 months or less on the balance sheet and recognize the associated lease payments in the consolidated statements of operations on a straight-line basis over the lease term. The Company is still assessing its existing lease contracts and the impact of the new leasing standards on its consolidated results of operations, financial position and disclosures. The Company currently expects the impact of adoption of the new leasing standards will have a material impact to the Company’s consolidated balance sheet in recognizing additional lease liabilities and right-of-use assets as of January 1, 2019 related to the Company’s operating leases. The Company does not expect that the new standard will have a material impact on its consolidated statements of operations or cash flows.

In August 2016, the FASB issued ASU No. 2016-15, Statement of Cash Flows: Classification of Certain Cash Receipts and Cash Payments. This guidance addresses the presentation and classification of certain cash receipts and cash payments in the statement of cash flows. This standard was effective for the Company in 2018. The adoption of this guidance had no impact on the Company’s consolidated financial statements as of and for the year ended December 31, 2018.

In May 2017, the FASB issued ASU No. 2017-09, Compensation – Stock Compensation: Scope of Modification Accounting. This guidance addresses which changes to the terms or conditions of a share-based payment award require an entity to apply modification accounting. This standard was effective for the Company in 2018. The adoption of this guidance had no impact on the Company’s consolidated financial statements as of and for the year ended December 31, 2018.

In June 2018, the FASB issued ASU No. 2018-07, Compensation—Stock Compensation (Topic 718): Improvements to Nonemployee Share-Based Payment Accounting. This ASU is intended to simplify aspects of share-based compensation issued to non-employees by making the guidance consistent accounting for employee share-based compensation. ASU 2018-07 is effective for annual periods beginning after December 15, 2018 and interim periods within those annual periods, with early adoption permitted. The Company is evaluating the effect that this guidance will have on its consolidated financial statements.

Fair Value Measurements and Marketable Securities

12 Months Ended

Dec. 31, 2018

Fair Value Disclosures [Abstract]

Fair Value Measurements and Marketable Securities

3. Fair Value Measurements and Marketable Securities

Fair Value Measurements

The following tables present information about the Company’s financial assets that have been measured at fair value as of December 31, 2018 and 2017 and indicate the fair value of the hierarchy of the valuation inputs utilized to determine such fair value. In general, fair values determined by Level 1 inputs utilize quoted prices (unadjusted) in active markets for identical assets or liabilities. Fair value determined by Level 2 inputs utilize observable inputs other than Level 1 prices, such as quoted prices for similar assets or liabilities, quoted market prices in markets that are not active or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the related assets or liabilities. Fair values determined by Level 3 inputs are unobservable data points for the asset or liability, and include situations where there is little, if any, market activity for the asset or liability. During the years ended December 31, 2018 and 2017, there were no transfers between Level 1 and Level 2 financial assets.

The following tables summarize the Company’s cash equivalents and marketable securities as of December 31, 2018 and 2017:

	December 31, 2018
			Quoted		Significant
			Prices in		Other		Significant
			Active		Observable		Unobservable
			Markets		Inputs		Inputs
	Total		(Level 1)		(Level 2)		(Level 3)
	(in thousands)
Cash equivalents:
Money market funds	$	40,231	$	40,231	$	—	$	—
Commercial paper		4,979		—		4,979		—
Total cash equivalents		45,210		40,231		4,979		—
Marketable securities:
Commercial paper		38,911		—		38,911		—
Corporate bonds		25,830		—		25,830		—
U.S. Government securities		3,994		—		3,994		—
Total marketable securities		68,735		—		68,735		—
Total cash equivalents and marketable securities	$	113,945	$	40,231	$	73,714	$	—

	December 31, 2017
			Quoted		Significant
			Prices in		Other		Significant
			Active		Observable		Unobservable
			Markets		Inputs		Inputs
	Total		(Level 1)		(Level 2)		(Level 3)
	(in thousands)
Cash equivalents:
Money market funds	$	15,802	$	15,802	$	—	$	—
Commercial paper		998		—		998		—
Corporate bonds		549		—		549		—
Total cash equivalents		17,349		15,802		1,547		—
Marketable securities:
Corporate bonds		50,844		—		50,844		—
Commercial paper		9,951		—		9,951		—
Certificates of deposit		480		—		480		—
Total marketable securities		61,275		—		61,275		—
Total cash equivalents and marketable securities	$	78,624	$	15,802	$	62,822	$	—

The carrying amounts reflected in the consolidated balance sheets for tax incentive receivable, accounts payable, and accrued expenses approximate fair value due to their short-term maturities. The carrying value of the Company’s outstanding notes payable approximates fair value (a Level 2 fair value measurement), reflecting interest rates currently available to the Company.

Marketable Securities

The following tables summarize the Company’s marketable securities as of December 31, 2018 and 2017:

	December 31, 2018
			Gross		Gross
	Amortized		Unrealized		Unrealized
	Cost		Gains		Losses			Fair Value
	(in thousands)
Assets:
Commercial paper (due within 1 year)		38,921		—		(10	)		38,911
Corporate bonds (due within 1 year)	$	25,851	$	3	$	(24	)	$	25,830
U.S. Government securities (due within 1 year)		3,995		—		(1	)		3,994
	$	68,767	$	3	$	(35	)	$	68,735

	December 31, 2017
			Gross		Gross
	Amortized		Unrealized		Unrealized
	Cost		Gains		Losses			Fair Value
	(in thousands)
Assets:
Corporate bonds (due within 1 year)	$	50,892	$	—	$	(48	)	$	50,844
Commercial paper (due within 1 year)		9,961		—		(10	)		9,951
Certificates of deposit (due within 1 year)		480		—		—			480
	$	61,333	$	—	$	(58	)	$	61,275

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References + Details

Property and Equipment, net

12 Months Ended

Dec. 31, 2018

Property Plant And Equipment [Abstract]

Property and Equipment, net

4. Property and Equipment, net

Property and equipment, net consisted of the following as of December 31, 2018 and 2017:

		December 31,
	Useful Life	2018			2017
		(in thousands)
Office equipment	3-5 years	$	348		$	421
Furniture and fixtures	5 years		156			194
Equipment	5 years		6			6
Leasehold improvements	*		415			415
			925			1,036
Less: Accumulated depreciation			(550	)		(508	)
		$	375		$	528

*	shorter of asset life or lease term

Depreciation expense was $0.3 million, $0.2 million and $0.2 million for the years ended December 31, 2018, 2017 and 2016, respectively.

Accrued Expenses

12 Months Ended

Dec. 31, 2018

Payables And Accruals [Abstract]

Accrued Expenses

5. Accrued Expenses

Accrued expenses consisted of the following as of December 31, 2018 and 2017:

	December 31,
	2018		2017
	(in thousands)
Accrued payroll and related expenses	$	2,291	$	2,229
Accrued research and development expenses		1,526		1,647
Accrued professional fees		221		292
Accrued other		223		105
	$	4,261	$	4,273

Notes Payable

12 Months Ended

Dec. 31, 2018

Debt Disclosure [Abstract]

Notes Payable

6. Notes Payable

On December 29, 2017, the Company entered into a loan and security agreement with Silicon Valley Bank (the “Term Loan”). The Term Loan provided for borrowings of $20.0 million. On December 29, 2017, the Company received proceeds of $20.0 million from the issuance of a promissory note. The promissory note issued under the Term Loan is collateralized by substantially all of the Company’s personal property, other than its intellectual property.

Upon entering into this Term Loan, the Company is obligated to make monthly, interest-only payments until March 29, 2019 and, thereafter, to pay 33 consecutive, equal monthly installments of principal and interest from April 1, 2019 through December 1, 2021. The outstanding Term Loan bears a variable annual interest rate of 1.25% above the prime rate, which at December 31, 2018 was 5.5%. In addition, a final payment equal to 8.0% of the Term Loan is due upon the earlier of the maturity date, acceleration of the Term Loan or prepayment of all or part of the Term Loan. The Company accrues the final payment amount of $1.6 million, to outstanding debt by charges to interest expense using the effective-interest method from the date of issuance through the maturity date. The effective annual interest rate of the outstanding debt under the Term Loan is approximately 9.9% as of December 31, 2018.

Additionally, the Company, as the borrower, is required to maintain a minimum cash, cash equivalents and marketable securities balance at Silicon Valley Bank of no less than 105% of the total outstanding principal balance of the Term Loan, which as of December 31, 2018 and 2017 was $21.0 million.

Further, as of 45 days after the Term Loan was entered in, the Company must maintain a balance of unrestricted cash, cash equivalents and marketable securities at Silicon Valley Bank in an amount not less than the greater of (i) $55.0 million and (ii) sixty-five percent (65%) of all the Company’s cash, cash equivalents and marketable securities. If the Company does not meet this requirement it will not be considered an event of default provided it immediately secures 87.5% of the principal balance in a restricted cash account.

There are negative covenants restricting the Company’s activities, including limitations on dispositions, mergers or acquisitions; encumbering or granting a security interest in its intellectual property; incurring indebtedness or liens; paying dividends; making certain investments; permit the aggregate value of cash maintained by its Australian subsidiary not to exceed $4.0 million and certain other business transactions.

The Term Loan also includes events of default, the occurrence and continuation of any of which provides the lenders the right to exercise remedies against the Company and the collateral securing the loans under the Term Loan, including cash in the amount of the outstanding balance. These events of default include, among other things, failure to pay any amounts due under the Term Loan, insolvency, the occurrence of a material adverse event, the occurrence of any default under certain other indebtedness and a final judgment against the Company in an amount greater than $0.3 million.

As of December 31, 2017, the Company had fully repaid all outstanding amounts due under a loan and security agreement with Oxford Finance LLC and Midcap Financial (the “2014 Credit Facility”) entered into in March 2014.

As of December 31, 2018 and 2017, notes payable consist of the following:

	December 31,
	2018			2017
	(in thousands)
Notes payable	$	20,000		$	20,000
Less: current portion		(5,455	)		—
Notes payable, net of current portion		14,545			20,000
Accretion related to final payment		640			—
Notes payable, long term	$	15,185		$	20,000

As of December 31, 2018, the estimated future principal payments due are as follows:

Year Ending December 31,
(in thousands)
2019	$	5,455
2020		7,273
2021		7,272
	$	20,000

During the years ended December 31, 2018 and 2017, the Company recognized $1.9 million and less than $0.1 million, respectively, of interest expense related to the Term Loan. During the years ended December 31, 2017 and 2016, the Company recognized $0.2 million and $0.5 million, respectively, of interest expense related to the 2014 Credit Facility.

Stockholders' Equity

12 Months Ended

Dec. 31, 2018

Equity [Abstract]

Stockholders' Equity

7. Stockholders’ Equity

On July 2, 2018, the Company completed a public offering of its common stock, which resulted in the sale of 9,200,000 shares at a price of $7.50 per share, resulting in net proceeds of approximately $64.6 million after deducting underwriting discounts and commissions, as well as offering costs.

On November 9, 2018, the Company entered into a sales agreement (the “Sales Agreement”) with Cowen and Company, LLC (“Cowen”), to sell shares of the Company’s common stock, with aggregate gross sales proceeds of up to $50.0 million, from time to time, through an at-the-market equity offering program under which Cowen will act as its sales agent (the “ATM Offering Program”). Cowen is entitled to compensation for its services equal to 3.0% of the gross proceeds of any shares of common stock sold through Cowen under the Sales Agreement. The Company has no obligation to sell any shares under the Sales Agreement, and may at any time suspend solicitation and offers under the Sales Agreement. The shares will be issued pursuant to the Company’s Registration Statement on Form S-3 filed on August 9, 2017 with the Securities and Exchange Commission (“SEC”). The Company filed a prospectus supplement, dated November 9, 2018, with the SEC in connection with the offer and sale of the shares pursuant to the Sales Agreement. As of December 31, 2018, the Company has not sold shares under the Sales Agreement.

As of December 31, 2018 and 2017, the Company’s Certificate of Incorporation, as amended and restated, authorizes the Company to issue 5,000,000 shares of $0.001 par value preferred stock. The rights, preferences, restrictions, qualifications and limitations of such stock are to be determined by the Company’s board of directors.

As of December 31, 2018 and 2017, the Company’s Certificate of Incorporation, as amended and restated, authorizes the Company to issue 115,000,000 shares of $0.001 par value common stock.

Stock-Based Awards

12 Months Ended

Dec. 31, 2018

Disclosure Of Compensation Related Costs Sharebased Payments [Abstract]

Stock-Based Awards

8. Stock-Based Awards

Stock Option Plan

The Company’s 2014 Stock Option and Incentive Plan (the “2014 Plan”) provides for the grant of stock options, stock appreciation rights, restricted stock awards, restricted stock units, unrestricted stock awards, performance-share awards, cash-based awards and dividend equivalent rights to employees, members of the board of directors and consultants of the Company. The number of shares initially reserved for issuance under the 2014 Plan was 2,168,221 shares of common stock. The number of shares reserved for issuance may be increased by the number of shares under the previously authorized 2006 Stock Option Plan that are not needed to fulfill the Company’s obligations for awards issued under the 2006 Stock Option Plan as a result of forfeiture, expiration, cancellation, termination or net issuances of awards thereunder. The number of shares of common stock that may be issued under the 2014 Plan is also subject to increase on the first day of each fiscal year by the lesser of (i) 4% of the Company’s outstanding shares of common stock as of that date, or (ii) an amount determined by the board of directors. As of December 31, 2018, 2,499,951 shares are available for grant under the 2014 Plan, including 1,099,578 shares automatically added to the 2014 Stock Option Plan on January 1, 2018.

Stock Option Grants

Option Grants with time-based vesting conditions

During the years ended December 31, 2018, 2017 and 2016, the Company granted 1,823,386, 1,214,874 and 1,527,559 stock options, respectively, under the 2014 Plan. The vesting of these awards is time-based and the restrictions typically lapse over periods of three to four years. Stock options were granted with exercise prices equal to the fair value of the Company’s common stock on the date of grant. The Company bases fair value of common stock on the quoted market price of the Company’s common stock. During the years ended December 31, 2018 and 2017 the Company granted 225,000 and 550,000 options, respectively, with time-based vesting as inducement grants outside of the 2014 Plan in accordance with NASDAQ Listing Rule 5635(c)(4). These stock options have a ten-year term and an exercise price equal to the closing price of the Company’s common stock on the grant date. The options vest as to 25% of the shares on the first anniversary of the grant date and the remainder in equal monthly installments thereafter over a 3-year period.

The fair value of each service-based stock option grant to employees and directors is estimated on the date of grant using the Black-Scholes option-pricing model. The Company estimates its expected volatility using a weighted average of the historical volatility of publicly-traded peer companies and its own common stock since its IPO in June 2014, and expects to continue to do so until such time as it has adequate historical data regarding the volatility of its own traded stock price for the duration of the expected term. The expected term of the Company’s stock options has been determined utilizing the “simplified” method for awards that qualify as “plain-vanilla” options. The risk-free interest rate is determined by reference to the U.S. Treasury yield curve in effect at the time of grant of the award for time periods approximately equal to the expected term of the award. Expected dividend yield is based on the fact that the Company has never paid cash dividends and does not expect to pay any cash dividends in the foreseeable future. The assumptions that the Company used to determine the fair value of the stock options granted to employees and directors are as follows, presented on a weighted average basis:

	2018			2017			2016
Risk-free interest rate		2.77	%		2.10	%		1.40	%
Expected term (in years)		6.17			6.17			6.18
Expected volatility		100	%		93	%		87	%
Expected dividend yield		0	%		0	%		0	%

The following table summarizes the Company’s stock option activity described above, since December 31, 2017:

	Shares			Weighted		Average
	Issuable			Average		Remaining	Aggregate
	Under			Exercise		Contractual	Intrinsic
	Options			Price		Term	Value
						(in years)	(in thousands)
Outstanding as of December 31, 2017		4,494,201		$	10.12	7.8	$	3,251
Granted		2,048,386		$	7.59
Exercised		(532,661	)	$	4.12
Forfeited		(985,555	)	$	14.58
Outstanding as of December 31, 2018		5,024,371		$	8.85	7.6	$	3,143
Options exercisable as of December 31, 2018		2,421,674		$	11.22	6.1	$	2,240

The aggregate intrinsic value was calculated based on the positive differences between the market value of the Company’s common stock and the exercise prices of the options. The aggregate intrinsic value of service-based stock options exercised was $1.6 million, $0.3 million and $0.1 million during the years ended December 31, 2018, 2017 and 2016, respectively.

The Company received cash proceeds from the exercise of stock options of $2.2 million, $0.1 million, and less than $0.1 million during the years ended December 31, 2018, 2017 and 2016, respectively.

The weighted average grant-date fair value of service-based stock options granted to employees and directors during the years ended December 31, 2018, 2017 and 2016 was $6.08, $2.91 and $4.86, per share, respectively.

As of December 31, 2018 and 2017, there were outstanding unvested service-based stock options held by nonemployees for the purchase of 45,209 and 77,567 shares of common stock, respectively.

Option Grants with market-based vesting conditions

In October 2017, the Company granted 687,500 common stock options that vest on the third anniversary of the grant date upon achievement by the Company of minimum common stock prices for 20 consecutive days during the Earning Period, the (“Price Target Options”). The Earning Period is defined as the period between the first anniversary of the grant date and the third anniversary of the grant date. Of the 687,500 Price Target Options granted in 2017, 137,500 were granted under the 2014 Stock Plan and 550,000 were granted to the newly-hired Chief Executive Officer as an inducement grant outside of the 2014 Plan in accordance with NASDAQ Listing Rule 5635(c)(4). These stock options have a ten-year term and an exercise price equal to the closing price of the Company’s common stock on the grant date. In August 2018, the 137,500 shares granted under the 2014 Stock Plan were forfeited.

The number of Price Target Options that will vest upon achievement of the target will vary based on the level of achievement from a maximum of 200% of the target shares to a threshold of 50% of the target shares, with no vesting, absent certain circumstances, if the threshold requirement is not achieved or the employee is no longer with the Company at the end of the three-year period. The Price Target Options are valued using Monte Carlo simulation models. The number of options expected to vest, based on achievement of the specified market condition, is factored into the grant date Monte Carlo valuations for the Price Target Options. Compensation expense is recognized ratably over the attribution period.

The assumptions that the Company used to determine the fair value of the Price Target Options granted to employees were as follows, presented on a weighted average basis:

	2017
Risk-free interest rate		2.24	%
Expected term (in years)		6.30
Expected volatility		95	%
Expected dividend yield		0	%

The Price Target Options had a grant date total fair value of $3.1 million and a weighted average fair value of $4.56 per share. As of December 31, 2018, the 550,000 Price Target Options had an aggregate intrinsic value of $0.9 million and a remaining contractual term of 8.77 years.

Restricted Stock Units

The Company has granted restricted stock units with time-based vesting conditions. The Company values restricted stock units on the grant-date using the market price of the Company’s common stock. The aggregate intrinsic value of restricted stock units that vested during the years ended December 31, 2018, 2017 and 2016 was $0.2 million, $0.1 million and $0.1 million respectively, calculated as the fair value of the Company’s common stock on the date it vests. During the years ended December 31, 2018, 2017 and 2016, the Company granted 17,856, 22,128 and 13,273 restricted stock units, respectively, all of which vested during 2018, 2017 and 2016, respectively, at a weighted average grant-date fair value of $5.18, $4.18 and $7.91, respectively. As of December 31, 2018 and 2017, there were no unvested restricted stock units outstanding.

2014 Employee Stock Purchase Plan

The Company has a 2014 Employee Stock Purchase Plan (the “ESPP”) under which a total of 265,000 shares of common stock were reserved for issuance. During both 2018 and 2017 there were two offering periods, January 1 through June 30 and July 1 through December 31. The per share purchase price for offerings is equal to the lesser of 85% of the closing market price of the Company’s common stock on the first day or last day of the offering period. The Company issued 46,181 and 43,781 shares during the years ended December 31, 2018 and 2017, respectively. As of December 31, 2018 and 2017, there are 129,835 and 176,016 shares, respectively, of common stock available for issuance to participating employees under the ESPP.

Stock-based Compensation

The Company recorded stock-based compensation expense related to stock options and restricted common stock in the following expense categories within its consolidated statements of operations:

	Year Ended December 31,
	2018		2017		2016
	(in thousands)
Research and development	$	5,476	$	4,138	$	3,543
General and administrative		4,151		4,163		6,390
	$	9,627	$	8,301	$	9,933

In addition, during the year ended December 31, 2016, in connection with its strategic restructuring further discussed in Note 14, the Company recorded a one-time, non-cash stock option modification expense of $0.2 million, which is included in the stock-based compensation expense line items of both the consolidated statements of cash flows and the consolidated statements of changes in stockholders’ equity.

As of December 31, 2018, the Company had unrecognized stock-based compensation expense related to its unvested service-based stock option awards of $10.8 million, which is expected to be recognized over the remaining weighted average vesting period of 2.2 years.

As of December 31, 2018, the Company had unrecognized stock-based compensation expense related to its unvested market-based stock option awards of $1.7 million, which is expected to be recognized over the remaining weighted average vesting period of 1.8 years.

Net Loss Per Share

12 Months Ended

Dec. 31, 2018

Earnings Per Share [Abstract]

Net Loss Per Share

9. Net Loss Per Share

Basic and diluted net loss per share was calculated as follows:

	Year Ended December 31,
	2018			2017			2016
	(in thousands, except per share data)
Basic and diluted net loss per share:
Numerator:
Net loss	$	(61,368	)	$	(52,028	)	$	(57,878	)
Denominator:
Weighted average common shares outstanding, basic and diluted		32,228,721			27,433,239			27,297,934
Net loss per share, basic and diluted	$	(1.90	)	$	(1.90	)	$	(2.12	)

The Company excluded the following common stock equivalents, outstanding as of December 31, 2018, 2017 and 2016, from the computation of diluted net loss per share for the years ended December 31, 2018, 2017 and 2016 because they had an anti-dilutive impact due to the net loss incurred for the periods:

	As of December 31,
	2018		2017		2016
Options to purchase common stock		5,024,371		4,494,201		3,115,003

Commitments and Contingencies

12 Months Ended

Dec. 31, 2018

Commitments And Contingencies Disclosure [Abstract]

Commitments and Contingencies

10. Commitments and Contingencies

Leases

The Company has a lease for office space in Boston, Massachusetts, effective as of July 28, 2014, with a term expiring July 31, 2020. In March 2015, the Company entered into an operating lease for additional office space in Boston, Massachusetts, effective as of April 15, 2015, with a term expiring on July 31, 2020, and an option to extend this lease for three additional years. In addition, with the landlord’s consent, the Company has subleased 2,976 square feet of office space in Boston, Massachusetts to an unrelated third party beginning on January 1, 2017 and expiring on June 30, 2020, and the Company expects to receive approximately $0.2 million in sublease rental income from January 1, 2019 through the end of the sublease term. In October 2015, the Company entered into an operating lease for office space in San Diego, California, effective as of October 1, 2015, with a term expiring on September 30, 2019, and an option to extend this lease for five additional years.

Future minimum lease payments for its operating leases as of December 31, 2018 were as follows:

Year Ending December 31,
(in thousands)
2019	$	464
2020		226
2021		—
2022		—
	$	690

During the years ended December 31, 2018, 2017 and 2016, the Company recognized $0.4 million, $0.3 million and $0.4 million, respectively, of rental expense related to office space.

Intellectual Property Licenses

The Company has acquired exclusive rights to develop patented compounds and related know-how for beloranib under two licensing agreements with two third parties in the course of its research and development activities. The licensing rights obligate the Company to make payments to the licensors for license fees, milestones, license maintenance fees and royalties. The Company is also responsible for patent prosecution costs.

As of December 31, 2018, the Company is obligated to make additional milestone payments of up to $12.3 million upon reaching certain pre-commercialization milestones, such as clinical trials and government approvals (including the U.S. Food and Drug Administration, or “FDA”, approval of a New Drug application, or “NDA”), and up to $12.5 million upon reaching certain product commercialization milestones related to the development of beloranib. Under one of the license agreements, the Company is also obligated to pay up to $1.3 million with respect to each subsequent licensed product, if any, that is a new chemical entity. In addition, the Company will owe single-digit royalties on sales of commercial products developed using these licensed technologies, if any.

There were no milestones achieved during the years ended December 31, 2018, 2017 or 2016. The Company is also obligated to pay to the licensors a percentage of fees received if and when the Company sublicenses the technology. As of December 31, 2018, the Company has not yet developed a commercial product using the licensed technologies and it has not entered into any sublicense agreements for the technologies.

Indemnification Agreements

In the ordinary course of business, the Company may provide indemnification of varying scope and terms to vendors, lessors, business partners, and other parties with respect to certain matters including, but not limited to, losses arising out of breach of such agreements or from intellectual property infringement claims made by third parties. In addition, the Company has entered into indemnification agreements with members of management team and the board of directors of the Company that will require the Company, among other things, to indemnify them against certain liabilities that may arise by reason of their status or service as directors or officers. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is, in many cases, unlimited. To date, the Company has not incurred any material costs as a result of such indemnifications. The Company does not believe that the outcome of any claims under indemnification arrangements will have a material effect on its financial position, results of operations or cash flows, and it has not accrued any liabilities related to such obligations in its consolidated financial statements as of December 31, 2018.

Legal Proceedings

The Company accrues a liability for legal contingencies when it believes that it is both probable that a liability has been incurred and that the Company can reasonably estimate the amount of the loss. The Company reviews these accruals and adjusts them to reflect ongoing negotiations, settlements, rulings, advice of legal counsel and other relevant information. To the extent new information is obtained and the views on the probable outcomes of claims, suits, assessments, investigations or legal proceedings change, changes in the Company’s accrued liabilities would be recorded in the period in which such determination is made. In addition, in accordance with the relevant authoritative guidance, for any matters in which the likelihood of material loss is at least reasonably possible, the Company will provide disclosure of the possible loss or range of loss. If a reasonable estimate cannot be made, however, the Company will provide disclosure to that effect. The Company expenses legal costs as they are incurred.

The Company may periodically become subject to other legal proceedings and claims arising in connection with ongoing business activities, including claims or disputes related to patents that have been issued or that are pending in the field of research on which the Company is focused. Other than the above action, the Company is not aware of any other material claims as of December 31, 2018.

Income Taxes

12 Months Ended

Dec. 31, 2018

Income Tax Disclosure [Abstract]

Income Taxes

11. Income Taxes

During the years ended December 31, 2018, 2017 and 2016, the Company recorded no income tax benefits for the net operating losses incurred in each year due to its uncertainty of realizing a benefit from those items.

The domestic and foreign components of loss before income taxes are as follows:

	Year Ended December 31,
	2018			2017			2016
	(in thousands)
Domestic	$	(58,708	)	$	(49,954	)	$	(57,799	)
Foreign		(2,660	)		(2,074	)		(79	)
Loss before income taxes	$	(61,368	)	$	(52,028	)	$	(57,878	)

A reconciliation of the U.S. federal statutory income tax rate to the Company’s effective income tax rate is as follows:

	Year Ended December 31,
	2018			2017			2016
Federal statutory income tax rate	(21.0%		)	(34.0%)			(34.0%)
Federal and state research and development tax credit		(4.2	)	(4.1)			(2.9)
State taxes, net of federal benefit		(3.7	)	(2.4)			(3.9)
Orphan drug tax credit		0.0			0.0		(1.3)
Stock compensation expense		5.1			1.5			0.7
Nondeductible Australia research and development expenses		0.9			1.4			0.0
Impact of federal rate change related to tax reform		0.0			65.2			0.0
Other items		0.0			1.2			1.3
Change in deferred tax asset valuation allowance		22.9		(28.8)				40.1
Effective income tax rate		0.0	%		0.0	%		0.0	%

Net deferred tax assets as of December 31, 2018 and 2017 consisted of the following:

	December 31,
	2018			2017
	(in thousands)
Noncurrent deferred tax assets:
Capitalized research and development expenses	$	58,832		$	49,325
Net operating loss carryforwards		16,728			13,848
Tax credit carryforwards		19,331			16,759
Capitalized legal expenses		1,918			1,646
Stock-based compensation		4,371			5,568
Accrued expenses		493			522
Other temporary differences		19			13
Total noncurrent deferred tax assets		101,692			87,681
Total gross deferred tax assets		101,692			87,681
Valuation allowance		(101,692	)		(87,681	)
Net deferred tax assets	$	—		$	—

Changes in the valuation allowance for deferred tax assets during the years ended December 31, 2018, 2017 and 2016 related primarily to changes in net operating loss carryforwards, capitalized research and development expenses and tax credit carryforwards and were as follows:

	Year Ended December 31,
	2018		2017			2016
	(in thousands)
Valuation allowance as of beginning of year	$	87,681	$	97,720		$	74,541
Decreases recorded as benefit to income tax provision		—		(10,039	)		—
Increases recorded to income tax provision		14,011		—			23,179
Valuation allowance as of end of year	$	101,692	$	87,681		$	97,720

As of December 31, 2018, the Company had net operating loss carryforwards that expire for federal and state income tax purposes of $55.7 million and $48.0 million, respectively, which begin to expire in 2026 and 2030, respectively. As of December 31, 2018, the Company had net operating loss carryforwards that were generated after December 31, 2017 of $9.5 million that do not expire. As of December 31, 2018, the Company also had available tax credit carryforwards for federal and state income tax purposes of $16.6 million and $3.4 million, respectively, which begin to expire in 2026 and 2022, respectively. Utilization of the net operating loss carryforwards and tax credit carryforwards may be subject to a substantial annual limitation under Section 382 of the Internal Revenue Code of 1986 due to ownership changes that have occurred previously or that could occur in the future. These ownership changes may limit the amount of carryforwards that can be utilized annually to offset future taxable income.

In general, an ownership change, as defined by Section 382, results from transactions increasing the ownership of certain stockholders or public groups in the stock of a corporation by more than 50% over a three-year period. The Company has not conducted a study to assess whether a change of control has occurred or whether there have been multiple changes of control since inception due to the significant complexity and cost associated with such a study. If the Company has experienced a change of control, as defined by Section 382, at any time since inception, utilization of the net operating loss carryforwards or tax credit carryforwards would be subject to an annual limitation under Section 382, which is determined by first multiplying the value of the Company’s stock at the time of the ownership change by the applicable long-term tax-exempt rate, and then could be subject to additional adjustments, as required. Any limitation may result in expiration of a portion of the net operating loss carryforwards or tax credit carryforwards before utilization. Further, until a study is completed and any limitation is known, no amounts are being presented as an uncertain tax position.

As of December 31, 2018 and 2017, the Company’s gross deferred tax asset balance of $101.7 million and $87.7 million, respectively, was comprised principally of net operating loss carryforwards, capitalized research and development expenses and tax credit carryforwards. During the years ended December 31, 2018, 2017 and 2016, gross deferred tax assets increased (decreased) due to additional net operating loss carryforwards, research and development tax credits generated and additional research and development expenses capitalized for tax purposes and the effects of tax reform.

The Company has evaluated the positive and negative evidence bearing upon its ability to realize the deferred tax assets. Management has considered the Company’s history of cumulative net losses incurred since inception and its lack of commercialization of any products or generation of any revenue from product sales since inception and has concluded that it is more likely than not that the Company will not realize the benefits of the deferred tax assets. Accordingly, a full valuation allowance has been established against the deferred tax assets as of December 31, 2018 and 2017. Management reevaluates the positive and negative evidence at each reporting period.

The Company has not recorded any amounts for unrecognized tax benefits as of December 31, 2018 and 2017.

The Company files tax returns as prescribed by the tax laws of the jurisdictions in which it operates. In the normal course of business, the Company is subject to examination by federal and state jurisdictions, where applicable. There are currently no pending income tax examinations. The Company’s tax years are still open under statute from 2014 to the present. Earlier years may be examined to the extent that tax credit or net operating loss carryforwards are used in future periods. The Company’s policy is to record interest and penalties related to income taxes as part of its income tax provision.

On December 22, 2017, the Tax Cuts and Jobs Act (“TCJA”) was signed into U.S. law. The TCJA includes a number of changes to existing tax law, including, among other things, a permanent reduction in the federal corporate income tax rate from a top marginal rate of 35% down to a flat rate of 21%, effective as of January 1, 2018, as well as limitation of the deduction for net operating losses to 80% of annual taxable income and elimination of net operating loss carrybacks, in each case, for losses arising in taxable years beginning after December 31, 2017 (though any such net operating losses may be carried forward indefinitely).

As a result of the TCJA, the Company was required to revalue deferred tax assets and liabilities at 21%. This revaluation in 2017 resulted in a provision of $33.8 million to income tax expense in continuing operations and a corresponding reduction in the valuation allowance. There was no impact to the Company’s consolidated statements of operations and comprehensive loss as a result of the reduction in rates. The other provisions of the TCJA did not have a material impact on the Company’s consolidated financial statements. In accordance with authoritative guidance issued by the SEC, the income tax effect of the TCJA represents provisional amounts for which the Company’s accounting is incomplete but for which reasonable estimates were determined and recorded during the fourth quarter of 2017. The guidance provides for a measurement period, up to one year from the enactment date, in which provisional amounts may be adjusted when additional information is obtained, prepared and analyzed. During the year ended December 31, 2018, there were no changes made to the provisional amounts recognized in 2017 in connection with the enactment of the Tax Reform Act. The accounting for the income tax effects of the Tax Reform Act is complete as of December 31, 2018.

Retirement Plan

12 Months Ended

Dec. 31, 2018

Compensation And Retirement Disclosure [Abstract]

Retirement Plan

12. Retirement Plan

Effective January 1, 2018, the Company adopted a 401(k) plan for its employees. Under the terms of the plan, the Company contributes 3% of an employee’s annual base salary, up to a maximum of the annual Internal Revenue Service compensation limits, for all employees. The Company terminated its Savings Incentive Match Plan, or SIMPLE IRA as of December 31, 2017.

For the year ended December 31, 2018, the Company recognized $0.3 million of expense related to its contributions to the 401(k) plan.

During the years ended December 31, 2017 and 2016, the Company recognized $0.1 million and $0.2 million, respectively, of expense related to its contributions to the SIMPLE IRA.

Australia Research and Development Tax Incentive

12 Months Ended

Dec. 31, 2018

Research And Development [Abstract]

Australia Research and Development Tax Incentive

13. Australia Research and Development Tax Incentive

The Company’s wholly owned subsidiary, Zafgen Australia Pty Limited, which conducts core research and development activities on behalf of the Company, is eligible to receive a 43.5% refundable tax incentive for qualified research and development activities. For the years ended December 31, 2018, 2017 and 2016, $1.6 million, $0.9 million and $0.3 million, respectively, were recorded as a reduction to research and development expenses in the consolidated statements of operations. These amounts represented 43.5% for 2018 and 2017 and 45% for 2016, of the Company’s qualified research and development spending in Australia. The refund is denominated in Australian dollars and, therefore, the related receivable is re-measured into U.S. dollars as of each reporting date. For the years ended December 31, 2018, 2017 and 2016, the Company recorded in its consolidated statements of operations unrealized foreign currency exchange (losses) gains of $(0.2) million, $0.1 million, and less than $(0.1) million, respectively, related to this tax incentive receivable. As of December 31, 2018 and 2017, the Company’s tax incentive receivable from the Australian government was $1.5 million and $0.9 million, respectively.

Restructuring

12 Months Ended

Dec. 31, 2018

Restructuring And Related Activities [Abstract]

Restructuring

14. Restructuring

On July 19, 2016, the Company announced that following a comprehensive review of its assets and clinical programs, as well as feedback from regulatory authorities, the Company refocused its resources on development of a differentiated second-generation MetAP2 inhibitor, ZGN-1061. As part of the strategic restructuring, the Company reorganized its operations to align with its new priorities focused on ZGN-1061 development. The Company’s workforce was reduced by approximately 31% as of December 2016.

During the year ended December 31, 2016, the Company recorded $1.4 million of restructuring-related costs in operating expenses, including employee severance, benefits and related costs, as well as a stock option modification. The stock option modification was a one-time, non-cash expense of $0.2 million and is included in the stock-based compensation expense line items of both the consolidated statements of cash flows and the consolidated statements of changes in stockholders’ equity as of December 31, 2016. The Company does not expect to incur any additional significant costs associated with this restructuring.

The following table summarizes the restructuring costs by category for the periods indicated:

	Year Ended December 31, 2016
	(in thousands)
	Cash		Non-Cash		Total
Research and development	$	455	$	7	$	462
General and administrative		768		173		941
	$	1,223	$	180	$	1,403

The following table summarizes the restructuring reserve for the periods indicated:

	Year Ended
	December 31, 2017
	(in thousands)
Restructuring reserve beginning balance	$	376
Restructuring expenses incurred during the period		24
Amounts paid during the period		(400	)
Restructuring reserve ending balance	$	—

Quarterly Financial Data (Unaudited)

12 Months Ended

Dec. 31, 2018

Quarterly Financial Information Disclosure [Abstract]

Quarterly Financial Data (Unaudited)

15. Quarterly Financial Data (Unaudited)

The following information has been derived from unaudited consolidated financial statements that, in the opinion of management, include all recurring adjustments necessary for a fair statement of such information.

	Three Months Ended
	March 31,			June 30,			September 30,			December 31,
	2018			2018			2018			2018
	(in thousands, except per share data)
Revenue	$	—		$	—		$	—		$	—
Operating expenses		15,702			15,560			15,169			14,691
Net loss		(15,956	)		(15,775	)		(15,067	)		(14,570	)
Net loss per share, basic and diluted	$	(0.58	)	$	(0.57	)	$	(0.41	)	$	(0.39	)
Weighted average common shares outstanding, basic and diluted		27,541,594			27,565,064			36,619,575			37,036,065


	Three Months Ended
	March 31,			June 30,			September 30,			December 31,
	2017			2017			2017			2017
	(in thousands, except per share data)
Revenue	$	—		$	—		$	—		$	—
Operating expenses		13,265			13,536			12,840			13,358
Net loss		(13,011	)		(13,347	)		(12,585	)		(13,085	)
Net loss per share, basic and diluted	$	(0.48	)	$	(0.49	)	$	(0.46	)	$	(0.48	)
Weighted average common shares outstanding, basic and diluted		27,350,673			27,407,408			27,483,550			27,489,397

Subsequent Events

12 Months Ended

Dec. 31, 2018

Subsequent Events [Abstract]

Subsequent Events

16. Subsequent Events

On February 12, 2019, the Company entered into an operating lease with Shigo Center Plaza Owners, LLC, for approximately 17,705 square feet of office space for a new headquarters located at 1-3 Center Plaza, Boston, Massachusetts. The lease has a term of 124 months, and the Company has an option to extend this lease for 60 additional months. As part of the agreement the Company is required to maintain a letter of credit, which upon signing was $1.3 million. Under the agreement, the Company will pay a monthly rent starting four months after the Commencement Date as set forth below.


	Monthly
Lease Year:	Base Rent
1	$	82,623
2	$	84,099
3	$	85,574
4	$	87,050
5	$	88,525
6	$	90,000
7	$	91,476
8	$	92,951
9	$	94,427
10	$	95,902

Summary of Significant Accounting Policies (Policies)	12 Months Ended
Summary of Significant Accounting Policies (Policies)	Dec. 31, 2018
Accounting Policies [Abstract]
Use of Estimates	Use of Estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities as of the date of the consolidated financial statements, and the reported amounts of expenses during the reporting periods. Significant estimates and assumptions reflected in these consolidated financial statements include, but are not limited to, the accrual of research and development expenses and the valuation of stock-based awards. Estimates are periodically reviewed in light of changes in circumstances, facts and experience. Actual results could differ from the Company’s estimates.
Cash Equivalents	Cash Equivalents The Company considers all short-term, highly liquid investments with original maturities of ninety days or less at acquisition date to be cash equivalents. Cash equivalents, which consist of money market funds, U.S. government securities, corporate bonds, and commercial paper, are stated at fair value.
Concentration of Credit Risk and of Significant Suppliers	Concentration of Credit Risk and of Significant Suppliers Financial instruments that potentially expose the Company to concentrations of credit risk consist primarily of cash, cash equivalents and marketable securities. The Company has all cash, cash equivalents and marketable securities balances at three accredited financial institutions in amounts that exceed federally insured limits. The Company does not believe that it is subject to unusual credit risk beyond the normal credit risk associated with commercial banking relationships. The Company is dependent on third-party manufacturers to supply products for research and development activities in its programs. In particular, the Company relies and expects to continue to rely on a small number of manufacturers to supply it with its requirements for the active pharmaceutical ingredients and formulated drugs related to these programs. These programs could be adversely affected by a significant interruption in the supply of active pharmaceutical ingredients and formulated drugs.
Marketable securities	Marketable Securities Marketable securities consist of investments with original maturities greater than ninety days. The Company has classified its investments with maturities beyond one year as short term, based on their highly liquid nature and because such marketable securities represent the investment of cash that is available for current operations. The Company classifies its marketable securities as available-for-sale. Accordingly, these investments are recorded at fair value, which is based on quoted market prices. Unrealized gains and losses are reported as a component of accumulated other comprehensive loss in stockholders’ equity. Realized gains and losses and declines in value judged to be other than temporary are included as a component of other income (expense), net, based on the specific identification method. When determining whether a decline in value is other than temporary, the Company considers various factors, including whether the Company has the intent to sell the security, and whether it is more likely than not that the Company will be required to sell the security prior to recovery of its amortized cost basis. Fair value is determined based on quoted market prices.
Deferred Offering Costs	Deferred Offering Costs The Company capitalizes certain legal, accounting and other third-party fees that are directly associated with in-process equity financings as other assets until such financings are consummated. After consummation of the equity financing, these costs are recorded in stockholders’ equity as a reduction of additional paid-in capital generated as a result of the offering or as a reduction to the carrying value of preferred stock issued.
Property and Equipment	Property and Equipment Property and equipment are stated at cost less accumulated depreciation. Depreciation expense is recognized using the straight-line method over a three or five-year estimated useful life for equipment, furniture and fixtures and office equipment. Leasehold improvements are amortized over the shorter of the asset life or the term of the lease agreement. Expenditures for repairs and maintenance of assets are charged to expense as incurred. Upon retirement or sale, the cost and related accumulated depreciation of assets disposed of are removed from the accounts and any resulting gain or loss is included in loss from operations.
Impairment of Long-Lived Assets	Impairment of Long-Lived Assets Long-lived assets consist of property and equipment. Long-lived assets to be held and used are tested for recoverability whenever events or changes in business circumstances indicate that the carrying amount of the assets may not be fully recoverable. Factors that the Company considers in deciding when to perform an impairment review include significant underperformance of the business in relation to expectations, significant negative industry or economic trends, and significant changes or planned changes in the use of the assets. If an impairment review is performed to evaluate a long-lived asset for recoverability, the Company compares forecasts of undiscounted cash flows expected to result from the use and eventual disposition of the long-lived asset to its carrying value. An impairment loss would be recognized when estimated undiscounted future cash flows expected to result from the use of an asset are less than its carrying amount. The impairment loss would be based on the excess of the carrying value of the impaired asset over its fair value, determined based on discounted cash flows. To date, the Company has not recorded any impairment losses on long-lived assets.
Research and Development Costs	Research and Development Costs Research and development costs are expensed as incurred. Included in research and development expenses are wages, stock-based compensation and benefits of employees, third-party license fees and milestones and other operational costs related to the Company’s research and development activities, including facility-related expenses and external costs of outside vendors engaged to conduct nonclinical studies, manufacturing activities, and clinical trials. The Company records research and development expenses net of any research and development tax incentives the Company is entitled to receive from government authorities.
Research Contract Costs and Accruals	Research Contract Costs and Accruals The Company has entered into various research and development contracts with research institutions and other companies both inside and outside of the United States. These agreements are generally cancelable, and related payments are recorded as research and development expenses as incurred. The Company records accruals for estimated ongoing research costs. When evaluating the adequacy of the accrued liabilities, the Company analyzes progress of the studies, including the phase or completion of events, invoices received and contracted costs. Significant judgments and estimates are made in determining the accrued balances at the end of any reporting period. Actual results could differ from the Company’s estimates. The Company’s historical accrual estimates have not been materially different from the actual costs.
Patent Costs	Patent Costs All patent-related costs incurred in connection with filing and prosecuting patent applications are recorded as general and administrative expenses as incurred, as recoverability of such expenditures is uncertain.
Accounting for Stock-Based Compensation	Accounting for Stock-Based Compensation The Company measures all stock-based awards granted to employees and directors based on the fair value on the date of grant using the Black-Scholes option-pricing model. Compensation expense of those awards is recognized over the requisite service period, which is generally the vesting period of the respective award. Typically, the Company issues awards with only service-based and market-based vesting conditions and records the expense for these awards using the straight-line method. The Company accounts for forfeitures as they occur. For stock-based awards granted to non-employee consultants, compensation expense is recognized over the period during which services are rendered by such consultants until completed. At the end of each financial reporting period prior to completion of the service, the fair value of these awards is re-measured using the then-current fair value of the Company’s common shares and updated assumption inputs in the Black-Scholes option-pricing model. The Company classifies stock-based compensation expense in its consolidated statements of operations and comprehensive loss in the same manner in which the award recipient’s payroll costs are classified or in which the award recipient’s service payments are classified.
Income Taxes	Income Taxes The Company accounts for income taxes using the asset and liability method, which requires the recognition of deferred tax assets and liabilities for the expected future tax consequences of events that have been recognized in the consolidated financial statements or in the Company’s tax returns. Deferred taxes are determined based on the difference between the financial statement and tax basis of assets and liabilities using enacted tax rates in effect in the years in which the differences are expected to reverse. Changes in deferred tax assets and liabilities are recorded in the provision for income taxes. The Company assesses the likelihood that its deferred tax assets will be recovered from future taxable income and, to the extent it believes, based upon the weight of available evidence, that it is more likely than not that all or a portion of deferred tax assets will not be realized, a valuation allowance is established through a charge to income tax expense. Potential for recovery of deferred tax assets is evaluated by estimating the future taxable profits expected and considering prudent and feasible tax planning strategies. The Company accounts for uncertainty in income taxes recognized in the consolidated financial statements by applying a two-step process to determine the amount of tax benefit to be recognized. First, the tax position must be evaluated to determine the likelihood that it will be sustained upon external examination by the taxing authorities. If the tax position is deemed more-likely-than-not to be sustained, the tax position is then assessed to determine the amount of benefit to recognize in the consolidated financial statements. The amount of the benefit that may be recognized is the largest amount that has a greater than 50% likelihood of being realized upon ultimate settlement. The provision for income taxes includes the effects of any resulting tax reserves, or unrecognized tax benefits, that are considered appropriate as well as the related net interest and penalties.
Segment Data	Segment Data The Company manages its operations as a single segment for the purposes of assessing performance and making operating decisions. The Company is a biopharmaceutical company dedicated to significantly improving the health and well-being of patients affected by both rare and prevalent metabolic diseases including type 2 diabetes, PWS, liver diseases and potentially other metabolically related disorders. No revenue has been generated since inception, and all tangible assets are held in the United States.
Comprehensive Loss	Comprehensive Loss Comprehensive loss includes net loss as well as other changes in stockholders’ equity that result from transactions and economic events other than those with stockholders. For the years ended December 31, 2018, 2017 and 2016, the Company’s only element of other comprehensive loss was unrealized gain or (loss) on marketable securities.
Net Loss Per Share	Net Loss Per Share Basic net loss per share is computed by dividing the net loss attributable to common stockholders by the weighted average number of common shares outstanding for the period. Diluted net loss per share attributable to common stockholders is computed by dividing the diluted net loss attributable to common stockholders by the weighted average number of common shares, including potential dilutive common shares assuming the dilutive effect of outstanding stock options and unvested restricted common shares, as determined using the treasury stock method. For periods in which the Company has reported net losses, diluted net loss per common share attributable to common stockholders is the same as basic net loss per common share attributable to common stockholders, since dilutive common shares are not assumed to have been issued if their effect is antidilutive.
Recently Issued and Adopted Accounting Pronouncements	Recently Issued and Adopted Accounting Pronouncements In February 2016, the Financial Accounting Standards Board (the “FASB”) issued ASU No. 2016-02, Leases, and in July 2018, the FASB issued ASU No. 2018-11, Leases (Topic 842): Targeted Improvements. The new leasing standards generally require lessees to recognize operating and financing lease liabilities and corresponding right-of-use assets on the consolidated balance sheet and to provide enhanced disclosures surrounding the amount, timing and uncertainty of cash flows arising from leasing arrangements. The Company will adopt the new standard effective January 1, 2019 and will not restate comparative periods. Presentation of leases within the consolidated statements of operations and comprehensive loss and consolidated statements of cash flows will be generally consistent with the current lease accounting guidance. The Company will elect the package of practical expedients permitted under the transition guidance and as such, the adoption of this ASU will not change the classification of any of the Company’s leases. The Company will elect to combine lease and non-lease components, elect not to record leases with an initial term of 12 months or less on the balance sheet and recognize the associated lease payments in the consolidated statements of operations on a straight-line basis over the lease term. The Company is still assessing its existing lease contracts and the impact of the new leasing standards on its consolidated results of operations, financial position and disclosures. The Company currently expects the impact of adoption of the new leasing standards will have a material impact to the Company’s consolidated balance sheet in recognizing additional lease liabilities and right-of-use assets as of January 1, 2019 related to the Company’s operating leases. The Company does not expect that the new standard will have a material impact on its consolidated statements of operations or cash flows. In August 2016, the FASB issued ASU No. 2016-15, Statement of Cash Flows: Classification of Certain Cash Receipts and Cash Payments. This guidance addresses the presentation and classification of certain cash receipts and cash payments in the statement of cash flows. This standard was effective for the Company in 2018. The adoption of this guidance had no impact on the Company’s consolidated financial statements as of and for the year ended December 31, 2018. In May 2017, the FASB issued ASU No. 2017-09, Compensation – Stock Compensation: Scope of Modification Accounting. This guidance addresses which changes to the terms or conditions of a share-based payment award require an entity to apply modification accounting. This standard was effective for the Company in 2018. The adoption of this guidance had no impact on the Company’s consolidated financial statements as of and for the year ended December 31, 2018. In June 2018, the FASB issued ASU No. 2018-07, Compensation—Stock Compensation (Topic 718): Improvements to Nonemployee Share-Based Payment Accounting. This ASU is intended to simplify aspects of share-based compensation issued to non-employees by making the guidance consistent accounting for employee share-based compensation. ASU 2018-07 is effective for annual periods beginning after December 15, 2018 and interim periods within those annual periods, with early adoption permitted. The Company is evaluating the effect that this guidance will have on its consolidated financial statements.

Fair Value Measurements and Marketable Securities (Tables)

12 Months Ended

Dec. 31, 2018

Fair Value Disclosures [Abstract]

Summary of Cash Equivalents and Marketable Securities

The following tables summarize the Company’s cash equivalents and marketable securities as of December 31, 2018 and 2017:

	December 31, 2018
			Quoted		Significant
			Prices in		Other		Significant
			Active		Observable		Unobservable
			Markets		Inputs		Inputs
	Total		(Level 1)		(Level 2)		(Level 3)
	(in thousands)
Cash equivalents:
Money market funds	$	40,231	$	40,231	$	—	$	—
Commercial paper		4,979		—		4,979		—
Total cash equivalents		45,210		40,231		4,979		—
Marketable securities:
Commercial paper		38,911		—		38,911		—
Corporate bonds		25,830		—		25,830		—
U.S. Government securities		3,994		—		3,994		—
Total marketable securities		68,735		—		68,735		—
Total cash equivalents and marketable securities	$	113,945	$	40,231	$	73,714	$	—

	December 31, 2017
			Quoted		Significant
			Prices in		Other		Significant
			Active		Observable		Unobservable
			Markets		Inputs		Inputs
	Total		(Level 1)		(Level 2)		(Level 3)
	(in thousands)
Cash equivalents:
Money market funds	$	15,802	$	15,802	$	—	$	—
Commercial paper		998		—		998		—
Corporate bonds		549		—		549		—
Total cash equivalents		17,349		15,802		1,547		—
Marketable securities:
Corporate bonds		50,844		—		50,844		—
Commercial paper		9,951		—		9,951		—
Certificates of deposit		480		—		480		—
Total marketable securities		61,275		—		61,275		—
Total cash equivalents and marketable securities	$	78,624	$	15,802	$	62,822	$	—

Summary of Marketable Securities

The following tables summarize the Company’s marketable securities as of December 31, 2018 and 2017:

	December 31, 2018
			Gross		Gross
	Amortized		Unrealized		Unrealized
	Cost		Gains		Losses			Fair Value
	(in thousands)
Assets:
Commercial paper (due within 1 year)		38,921		—		(10	)		38,911
Corporate bonds (due within 1 year)	$	25,851	$	3	$	(24	)	$	25,830
U.S. Government securities (due within 1 year)		3,995		—		(1	)		3,994
	$	68,767	$	3	$	(35	)	$	68,735

	December 31, 2017
			Gross		Gross
	Amortized		Unrealized		Unrealized
	Cost		Gains		Losses			Fair Value
	(in thousands)
Assets:
Corporate bonds (due within 1 year)	$	50,892	$	—	$	(48	)	$	50,844
Commercial paper (due within 1 year)		9,961		—		(10	)		9,951
Certificates of deposit (due within 1 year)		480		—		—			480
	$	61,333	$	—	$	(58	)	$	61,275

Property and Equipment, net (Tables)

12 Months Ended

Dec. 31, 2018

Property Plant And Equipment [Abstract]

Schedule of Property Plant and Equipment Net

Property and equipment, net consisted of the following as of December 31, 2018 and 2017:

		December 31,
	Useful Life	2018			2017
		(in thousands)
Office equipment	3-5 years	$	348		$	421
Furniture and fixtures	5 years		156			194
Equipment	5 years		6			6
Leasehold improvements	*		415			415
			925			1,036
Less: Accumulated depreciation			(550	)		(508	)
		$	375		$	528

*	shorter of asset life or lease term

Accrued Expenses (Tables)

12 Months Ended

Dec. 31, 2018

Payables And Accruals [Abstract]

Schedule of Accrued Expenses

Accrued expenses consisted of the following as of December 31, 2018 and 2017:

	December 31,
	2018		2017
	(in thousands)
Accrued payroll and related expenses	$	2,291	$	2,229
Accrued research and development expenses		1,526		1,647
Accrued professional fees		221		292
Accrued other		223		105
	$	4,261	$	4,273

Notes Payable (Tables)

12 Months Ended

Dec. 31, 2018

Debt Disclosure [Abstract]

Schedule of Notes Payable

As of December 31, 2018 and 2017, notes payable consist of the following:

	December 31,
	2018			2017
	(in thousands)
Notes payable	$	20,000		$	20,000
Less: current portion		(5,455	)		—
Notes payable, net of current portion		14,545			20,000
Accretion related to final payment		640			—
Notes payable, long term	$	15,185		$	20,000

Schedule of Estimated Future Principal Payments

As of December 31, 2018, the estimated future principal payments due are as follows:

Year Ending December 31,
(in thousands)
2019	$	5,455
2020		7,273
2021		7,272
	$	20,000

Stock-Based Awards (Tables)

12 Months Ended

Dec. 31, 2018

Summary of Stock Option Activity

The following table summarizes the Company’s stock option activity described above, since December 31, 2017:

	Shares			Weighted		Average
	Issuable			Average		Remaining	Aggregate
	Under			Exercise		Contractual	Intrinsic
	Options			Price		Term	Value
						(in years)	(in thousands)
Outstanding as of December 31, 2017		4,494,201		$	10.12	7.8	$	3,251
Granted		2,048,386		$	7.59
Exercised		(532,661	)	$	4.12
Forfeited		(985,555	)	$	14.58
Outstanding as of December 31, 2018		5,024,371		$	8.85	7.6	$	3,143
Options exercisable as of December 31, 2018		2,421,674		$	11.22	6.1	$	2,240

Summary of Stock-Based Compensation Expense Related To Stock Options And Restricted Common Stock

The Company recorded stock-based compensation expense related to stock options and restricted common stock in the following expense categories within its consolidated statements of operations:

	Year Ended December 31,
	2018		2017		2016
	(in thousands)
Research and development	$	5,476	$	4,138	$	3,543
General and administrative		4,151		4,163		6,390
	$	9,627	$	8,301	$	9,933

Time-Based Vesting Conditions [Member]

Assumptions used to Determine Fair Value of Stock Options Granted

The assumptions that the Company used to determine the fair value of the stock options granted to employees and directors are as follows, presented on a weighted average basis:

	2018			2017			2016
Risk-free interest rate		2.77	%		2.10	%		1.40	%
Expected term (in years)		6.17			6.17			6.18
Expected volatility		100	%		93	%		87	%
Expected dividend yield		0	%		0	%		0	%

Market-Based Vesting Conditions [Member]

Assumptions used to Determine Fair Value of Stock Options Granted

The assumptions that the Company used to determine the fair value of the Price Target Options granted to employees were as follows, presented on a weighted average basis:

	2017
Risk-free interest rate		2.24	%
Expected term (in years)		6.30
Expected volatility		95	%
Expected dividend yield		0	%

Net Loss Per Share (Tables)

12 Months Ended

Dec. 31, 2018

Earnings Per Share [Abstract]

Computation of Basic and Diluted Earnings Per Share

Basic and diluted net loss per share was calculated as follows:

	Year Ended December 31,
	2018			2017			2016
	(in thousands, except per share data)
Basic and diluted net loss per share:
Numerator:
Net loss	$	(61,368	)	$	(52,028	)	$	(57,878	)
Denominator:
Weighted average common shares outstanding, basic and diluted		32,228,721			27,433,239			27,297,934
Net loss per share, basic and diluted	$	(1.90	)	$	(1.90	)	$	(2.12	)

Summary of Common Stock Equivalents Outstanding

	As of December 31,
	2018		2017		2016
Options to purchase common stock		5,024,371		4,494,201		3,115,003

Commitments and Contingencies (Tables)

12 Months Ended

Dec. 31, 2018

Commitments And Contingencies Disclosure [Abstract]

Schedule of Future Minimum Lease Payments for Operating Leases

Future minimum lease payments for its operating leases as of December 31, 2018 were as follows:

Year Ending December 31,
(in thousands)
2019	$	464
2020		226
2021		—
2022		—
	$	690

Income Taxes (Tables)

12 Months Ended

Dec. 31, 2018

Income Tax Disclosure [Abstract]

Schedule of Domestic and Foreign Components of Loss Before Income Taxes

The domestic and foreign components of loss before income taxes are as follows:

	Year Ended December 31,
	2018			2017			2016
	(in thousands)
Domestic	$	(58,708	)	$	(49,954	)	$	(57,799	)
Foreign		(2,660	)		(2,074	)		(79	)
Loss before income taxes	$	(61,368	)	$	(52,028	)	$	(57,878	)

Reconciliation of Federal Statutory Income Tax Rate

A reconciliation of the U.S. federal statutory income tax rate to the Company’s effective income tax rate is as follows:

	Year Ended December 31,
	2018			2017			2016
Federal statutory income tax rate	(21.0%		)	(34.0%)			(34.0%)
Federal and state research and development tax credit		(4.2	)	(4.1)			(2.9)
State taxes, net of federal benefit		(3.7	)	(2.4)			(3.9)
Orphan drug tax credit		0.0			0.0		(1.3)
Stock compensation expense		5.1			1.5			0.7
Nondeductible Australia research and development expenses		0.9			1.4			0.0
Impact of federal rate change related to tax reform		0.0			65.2			0.0
Other items		0.0			1.2			1.3
Change in deferred tax asset valuation allowance		22.9		(28.8)				40.1
Effective income tax rate		0.0	%		0.0	%		0.0	%

Schedule of Net Deferred Tax Assets

Net deferred tax assets as of December 31, 2018 and 2017 consisted of the following:

	December 31,
	2018			2017
	(in thousands)
Noncurrent deferred tax assets:
Capitalized research and development expenses	$	58,832		$	49,325
Net operating loss carryforwards		16,728			13,848
Tax credit carryforwards		19,331			16,759
Capitalized legal expenses		1,918			1,646
Stock-based compensation		4,371			5,568
Accrued expenses		493			522
Other temporary differences		19			13
Total noncurrent deferred tax assets		101,692			87,681
Total gross deferred tax assets		101,692			87,681
Valuation allowance		(101,692	)		(87,681	)
Net deferred tax assets	$	—		$	—

Summary Changes in the Valuation Allowance for Deferred Tax Assets

	Year Ended December 31,
	2018		2017			2016
	(in thousands)
Valuation allowance as of beginning of year	$	87,681	$	97,720		$	74,541
Decreases recorded as benefit to income tax provision		—		(10,039	)		—
Increases recorded to income tax provision		14,011		—			23,179
Valuation allowance as of end of year	$	101,692	$	87,681		$	97,720

Restructuring (Tables)

12 Months Ended

Dec. 31, 2018

Restructuring And Related Activities [Abstract]

Summary of Restructuring Costs by Category

The following table summarizes the restructuring costs by category for the periods indicated:

	Year Ended December 31, 2016
	(in thousands)
	Cash		Non-Cash		Total
Research and development	$	455	$	7	$	462
General and administrative		768		173		941
	$	1,223	$	180	$	1,403

Summary of Restructuring Reserve

The following table summarizes the restructuring reserve for the periods indicated:

	Year Ended
	December 31, 2017
	(in thousands)
Restructuring reserve beginning balance	$	376
Restructuring expenses incurred during the period		24
Amounts paid during the period		(400	)
Restructuring reserve ending balance	$	—

Quarterly Financial Data (Unaudited) (Tables)

12 Months Ended

Dec. 31, 2018

Quarterly Financial Information Disclosure [Abstract]

Schedule of Unaudited Consolidated Financial Statements

	Three Months Ended
	March 31,			June 30,			September 30,			December 31,
	2018			2018			2018			2018
	(in thousands, except per share data)
Revenue	$	—		$	—		$	—		$	—
Operating expenses		15,702			15,560			15,169			14,691
Net loss		(15,956	)		(15,775	)		(15,067	)		(14,570	)
Net loss per share, basic and diluted	$	(0.58	)	$	(0.57	)	$	(0.41	)	$	(0.39	)
Weighted average common shares outstanding, basic and diluted		27,541,594			27,565,064			36,619,575			37,036,065


	Three Months Ended
	March 31,			June 30,			September 30,			December 31,
	2017			2017			2017			2017
	(in thousands, except per share data)
Revenue	$	—		$	—		$	—		$	—
Operating expenses		13,265			13,536			12,840			13,358
Net loss		(13,011	)		(13,347	)		(12,585	)		(13,085	)
Net loss per share, basic and diluted	$	(0.48	)	$	(0.49	)	$	(0.46	)	$	(0.48	)
Weighted average common shares outstanding, basic and diluted		27,350,673			27,407,408			27,483,550			27,489,397

Subsequent Events (Tables)

12 Months Ended

Dec. 31, 2018

Subsequent Events [Abstract]

Schedule of Monthly Base Rent

Under the agreement, the Company will pay a monthly rent starting four months after the Commencement Date as set forth below.


	Monthly
Lease Year:	Base Rent
1	$	82,623
2	$	84,099
3	$	85,574
4	$	87,050
5	$	88,525
6	$	90,000
7	$	91,476
8	$	92,951
9	$	94,427
10	$	95,902

Nature of the Business and Basis of Presentation - Additional Information (Detail) - USD ($) $ / shares in Units, $ in Thousands		12 Months Ended	158 Months Ended
	Jul. 02, 2018	Dec. 31, 2018	Dec. 31, 2018	Dec. 31, 2017	Dec. 29, 2017
Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items]
Entity incorporation date		Nov. 22, 2005
Accumulated deficit		$ 350,945	$ 350,945	$ 289,577
Net proceeds from sale of securities			397,900
Total cash, cash equivalents and marketable securities		118,100	118,100
Term Loan [Member]
Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items]
Aggregate principal balance		20,000	20,000		$ 20,000
Loan agreement minimum liquidity required		$ 21,000	$ 21,000	$ 21,000
Public Offering [Member]
Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items]
Issuance of common stock	9,200,000
Share price per share	$ 7.50
Net proceeds from public offering, after underwriting discount, commission and offering expenses	$ 64,600

Summary of Significant Accounting Policies - Additional Information (Detail)	12 Months Ended
	Dec. 31, 2018 USD ($)
Summary Of Significant Accounting Policies [Line Items]
Impairment losses on long-lived assets	$ 0
Percentage of likelihood to be realized upon ultimate settlement, description	50.00%
Equipment, Furniture and Fixtures and Office Equipment [Member] \| Minimum [Member]
Summary Of Significant Accounting Policies [Line Items]
Estimated useful life	3 years
Equipment, Furniture and Fixtures and Office Equipment [Member] \| Maximum [Member]
Summary Of Significant Accounting Policies [Line Items]
Estimated useful life	5 years

Fair Value Measurements and Marketable Securities - Summary of Cash Equivalents and Marketable Securities (Detail) - USD ($) $ in Thousands	Dec. 31, 2018	Dec. 31, 2017
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	$ 45,210	$ 17,349
Marketable securities	68,735	61,275
Total cash equivalents and marketable securities	113,945	78,624
Quoted Prices in Active Markets, (Level 1) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	40,231	15,802
Total cash equivalents and marketable securities	40,231	15,802
Significant Other Observable Inputs (Level 2) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	4,979	1,547
Marketable securities	68,735	61,275
Total cash equivalents and marketable securities	73,714	62,822
Money Market Funds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	40,231	15,802
Money Market Funds [Member] \| Quoted Prices in Active Markets, (Level 1) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	40,231	15,802
Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	4,979	998
Marketable securities	38,911	9,951
Commercial Paper [Member] \| Significant Other Observable Inputs (Level 2) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	4,979	998
Marketable securities	38,911	9,951
Corporate Bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents		549
Marketable securities	25,830	50,844
Corporate Bonds [Member] \| Significant Other Observable Inputs (Level 2) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents		549
Marketable securities	25,830	50,844
U.S. Government Securities [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Marketable securities	3,994
U.S. Government Securities [Member] \| Significant Other Observable Inputs (Level 2) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Marketable securities	$ 3,994
Certificates of Deposit [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Marketable securities		480
Certificates of Deposit [Member] \| Significant Other Observable Inputs (Level 2) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Marketable securities		$ 480

Fair Value Measurements and Marketable Securities - Summary of Marketable Securities (Detail) - USD ($) $ in Thousands	Dec. 31, 2018	Dec. 31, 2017
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 68,767	$ 61,333
Gross Unrealized Gains	3
Gross Unrealized Losses	(35)	(58)
Fair Value	68,735	61,275
Corporate Bonds (Due within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	25,851	50,892
Gross Unrealized Gains	3
Gross Unrealized Losses	(24)	(48)
Fair Value	25,830	50,844
Commercial Paper (Due within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	38,921	9,961
Gross Unrealized Losses	(10)	(10)
Fair Value	38,911	9,951
U.S. Government Securities (Due within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	3,995
Gross Unrealized Losses	(1)
Fair Value	$ 3,994
Certificates of Deposit (Due Within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost		480
Fair Value		$ 480

Property and Equipment, Net - Schedule of Property Plant and Equipment Net (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017
Property, Plant and Equipment [Line Items]
Property and equipment, gross	$ 925	$ 1,036
Less: Accumulated depreciation	(550)	(508)
Property and equipment, net	375	528
Office Equipment [Member]
Property, Plant and Equipment [Line Items]
Property and equipment, gross	$ 348	421
Office Equipment [Member] \| Minimum [Member]
Property, Plant and Equipment [Line Items]
Property and equipment, Useful Life	3 years
Office Equipment [Member] \| Maximum [Member]
Property, Plant and Equipment [Line Items]
Property and equipment, Useful Life	5 years
Furniture and Fixtures [Member]
Property, Plant and Equipment [Line Items]
Property and equipment, Useful Life	5 years
Property and equipment, gross	$ 156	194
Equipment [Member]
Property, Plant and Equipment [Line Items]
Property and equipment, Useful Life	5 years
Property and equipment, gross	$ 6	6
Leasehold Improvements [Member]
Property, Plant and Equipment [Line Items]
Property and equipment, gross	$ 415	$ 415

Property and Equipment, net - Additional Information (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Property Plant And Equipment Capitalized Interest Costs [Abstract]
Depreciation expense	$ 261	$ 188	$ 212

Accrued Expenses - Schedule of Accrued Expenses (Detail) - USD ($) $ in Thousands	Dec. 31, 2018	Dec. 31, 2017
Payables And Accruals [Abstract]
Accrued payroll and related expenses	$ 2,291	$ 2,229
Accrued research and development expenses	1,526	1,647
Accrued professional fees	221	292
Accrued other	223	105
Total accrued expense	$ 4,261	$ 4,273

Notes Payable - Additional Information (Detail) - USD ($)		12 Months Ended
	Dec. 29, 2017	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Debt Instrument [Line Items]
Proceeds from issuance of notes payable	$ 20,000,000		$ 20,000,000
Unrestricted cash, cash equivalents and marketable securities		$ 118,100,000
Credit facility default amount		300,000
Maximum [Member]
Debt Instrument [Line Items]
Aggregate value of cash maintained by Australian subsidiary, limit		4,000,000
Term Loan [Member]
Debt Instrument [Line Items]
Maximum borrowings under term loan	$ 20,000,000	$ 20,000,000
Debt facility description		Upon entering into this Term Loan, the Company is obligated to make monthly, interest-only payments until March 29, 2019 and, thereafter, to pay 33 consecutive, equal monthly installments of principal and interest from April 1, 2019 through December 1, 2021. The outstanding Term Loan bears a variable annual interest rate of 1.25% above the prime rate, which at December 31, 2018 was 5.5%. In addition, a final payment equal to 8.0% of the Term Loan is due upon the earlier of the maturity date, acceleration of the Term Loan or prepayment of all or part of the Term Loan.
Debt maturity date	Dec. 01, 2021
Debt facility interest rate description		1.25% above the prime rate
Debt facility variable annual interest rate	1.25%
Debt facility effective interest rate		5.50%
Debt facility fee percentage	8.00%
Charges to interest expense of debt outstanding	$ 1,600,000
Debt facility effective interest rate		9.90%
Loan agreement minimum liquidity required		$ 21,000,000	21,000,000
Debt facility covenant description		Further, as of 45 days after the Term Loan was entered in, the Company must maintain a balance of unrestricted cash, cash equivalents and marketable securities at Silicon Valley Bank in an amount not less than the greater of (i) $55.0 million and (ii) sixty-five percent (65%) of all the Company’s cash, cash equivalents and marketable securities. If the Company does not meet this requirement it will not be considered an event of default provided it immediately secures 87.5% of the principal balance in a restricted cash account
Percentage of principal balance to be secured in restricted cash account for not to be considered an event of default		87.50%
Interest expense on term loan		$ 1,900,000
Term Loan [Member] \| Minimum [Member]
Debt Instrument [Line Items]
Percentage equivalent of cash, cash equivalents and marketable securities balance		105.00%
Unrestricted cash, cash equivalents and marketable securities		$ 55,000,000
Percentage of cash, cash equivalents and marketable securities		65.00%
Term Loan [Member] \| Maximum [Member]
Debt Instrument [Line Items]
Interest expense on term loan			100,000
Secured Debt [Member] \| 2014 Credit Facility [Member]
Debt Instrument [Line Items]
Interest expense on credit facility			$ 200,000	$ 500,000

Notes Payable - Schedule of Notes Payable (Detail) - USD ($) $ in Thousands	Dec. 31, 2018	Dec. 31, 2017
Debt Instruments [Abstract]
Notes payable	$ 20,000	$ 20,000
Less: current portion	(5,455)
Notes payable, net of current portion	14,545	20,000
Accretion related to final payment	640
Notes payable, long term	$ 15,185	$ 20,000

Notes Payable - Schedule of Estimated Future Principal Payments (Detail) $ in Thousands	Dec. 31, 2018 USD ($)
Debt Instruments [Abstract]
2019	$ 5,455
2020	7,273
2021	7,272
Total	$ 20,000

Stockholders' Equity - Additional Information (Detail) - USD ($)			12 Months Ended
	Nov. 09, 2018	Jul. 02, 2018	Dec. 31, 2018	Dec. 31, 2016	Dec. 31, 2017
Proceeds from offering, net of commissions and underwriting discounts			$ 64,860,000
Preferred stock, shares authorized			5,000,000		5,000,000
Preferred stock, par value			$ 0.001		$ 0.001
Common stock, shares authorized			115,000,000		115,000,000
Common stock, par value			$ 0.001		$ 0.001
Common Stock [Member]
Issuance of common stock			9,200,000	5,564
Public Offering [Member]
Issuance of common stock		9,200,000
Share price per share		$ 7.50
Proceeds from offering, net of commissions and underwriting discounts		$ 64,600,000
ATM Offering Program [Member] \| Cowen [Member]
Sales agreement, description			The Company has no obligation to sell any shares under the Sales Agreement, and may at any time suspend solicitation and offers under the Sales Agreement.
ATM Offering Program [Member] \| Cowen [Member] \| Common Stock [Member]
Issuance of common stock			0
Percentage of compensation for services equal to gross proceeds	3.00%
ATM Offering Program [Member] \| Cowen [Member] \| Common Stock [Member] \| Maximum [Member]
Aggregate gross sales proceeds under sales agreement	$ 50,000,000

Stock-Based Awards - Additional Information (Detail) - USD ($)			1 Months Ended	12 Months Ended
	Aug. 31, 2018	Jan. 01, 2018	Oct. 31, 2017	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock option modification non cash expense						$ 200,000
Time-Based Vesting Conditions [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock based compensation, stock options granted				2,048,386
Term of stock option				10 years
Stock option vesting percentage				25.00%
Stock option vesting description				The options vest as to 25% of the shares on the first anniversary of the grant date and the remainder in equal monthly installments thereafter over a 3-year period.
Aggregate intrinsic value of stock options exercised				$ 1,600,000	$ 300,000	$ 100,000
Proceeds from exercise of common stock options				$ 2,200,000	$ 100,000
Weighted average grant-date fair value of stock options granted				$ 6.08	$ 2.91	$ 4.86
Stock based compensation, stock options forfeited				985,555
Aggregate intrinsic value of Price Target Options				$ 3,143,000	$ 3,251,000
Average remaining contractual life				7 years 7 months 6 days	7 years 9 months 18 days
Time-Based Vesting Conditions [Member] \| Non Employee [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of outstanding unvested shares held by nonemployees				45,209	77,567
Time-Based Vesting Conditions [Member] \| Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Proceeds from exercise of common stock options						$ 100,000
Market-Based Vesting Conditions [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock based compensation, stock options granted			687,500		687,500
Common stock earning period			Company granted 687,500 common stock options that vest on the third anniversary of the grant date upon achievement by the Company of minimum common stock prices for 20 consecutive days during the Earning Period, the (“Price Target Options”).
Total fair value of Price Target Options				$ 3,100,000
Weighted average fair value of Price Target Options				$ 4.56
Market-Based Vesting Conditions [Member] \| Options to Purchase Common Stock [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting period of stock option				3 years
Market-Based Vesting Conditions [Member] \| CEO [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock based compensation, stock options granted					550,000
Term of stock option					10 years
Aggregate intrinsic value of Price Target Options				$ 900,000
Average remaining contractual life				8 years 9 months 7 days
Market-Based Vesting Conditions [Member] \| Minimum [Member] \| Options to Purchase Common Stock [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of shares that will vest upon achievement of the target, as a percentage				50.00%
Market-Based Vesting Conditions [Member] \| Maximum [Member] \| Options to Purchase Common Stock [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of shares that will vest upon achievement of the target, as a percentage				200.00%
Restricted Stock Units (RSUs) [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Aggregate intrinsic value of restricted stock units vested during the period				$ 200,000	$ 100,000	$ 100,000
Number of restricted stock units granted				17,856	22,128	13,273
Weighted average grant-date fair value of restricted stock units granted				$ 5.18	$ 4.18	$ 7.91
Number of restricted stock units unvested				0	0
Time Based Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Unrecognized stock-based compensation cost				$ 10,800,000
Stock-based compensation recognized weighted average period				2 years 2 months 12 days
Market Based Stock Option [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Unrecognized stock-based compensation cost				$ 1,700,000
Stock-based compensation recognized weighted average period				1 year 9 months 18 days
2014 Stock Option and Incentive Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares of common stock reserved for issuance				2,168,221
Percentage of outstanding shares of common stock				4.00%
Common stock available for issuance				2,499,951
Shares added to plan		1,099,578
2014 Stock Option and Incentive Plan [Member] \| Time-Based Vesting Conditions [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock based compensation, stock options granted				1,823,386	1,214,874	1,527,559
2014 Stock Option and Incentive Plan [Member] \| Time-Based Vesting Conditions [Member] \| Minimum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting period of stock option				3 years
2014 Stock Option and Incentive Plan [Member] \| Time-Based Vesting Conditions [Member] \| Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting period of stock option				4 years
2014 Stock Option and Incentive Plan [Member] \| Market-Based Vesting Conditions [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock based compensation, stock options granted					137,500
Term of stock option					10 years
Stock based compensation, stock options forfeited	137,500
Date of granted share forfeited				2018-08
Grants Outside of 2014 Plan [Member] \| Time-Based Vesting Conditions [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock based compensation, stock options granted				225,000	550,000
2014 Employee Stock Purchase Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares of common stock reserved for issuance				265,000
Common stock available for issuance				129,835	176,016
Commencement date of first offering period				Jan. 01, 2018	Jan. 01, 2017
End date of first offering period				Jun. 30, 2018	Jun. 30, 2017
Commencement date of second offering period				Jul. 01, 2018	Jul. 01, 2017
End date of second offering period				Dec. 31, 2018	Dec. 31, 2017
Stock-based awards, shares				46,181	43,781
2014 Employee Stock Purchase Plan [Member] \| Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Discount from market price of the company's common stock offering				85.00%

Stock-Based Awards - Assumptions used to Determine Fair Value of Stock Options Granted (Detail)	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Time-Based Vesting Conditions [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate	2.77%	2.10%	1.40%
Expected term (in years)	6 years 2 months 1 day	6 years 2 months 1 day	6 years 2 months 4 days
Expected volatility	100.00%	93.00%	87.00%
Expected dividend yield	0.00%	0.00%	0.00%
Market-Based Vesting Conditions [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate		2.24%
Expected term (in years)		6 years 3 months 18 days
Expected volatility		95.00%
Expected dividend yield		0.00%

Stock-Based Awards - Summary of Stock Option Activity (Detail) - Time-Based Vesting Conditions [Member] - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares issuable under options, beginning balance	4,494,201
Shares issuable under options, granted	2,048,386
Shares issuable under options, exercised	(532,661)
Shares issuable under options, forfeited	(985,555)
Shares issuable under options, ending balance	5,024,371	4,494,201
Shares issuable under options, options exercisable	2,421,674
Weighted-average exercise price, beginning balance	$ 10.12
Weighted-average exercise price, granted	7.59
Weighted-average exercise price, exercised	4.12
Weighted-average exercise price, forfeited	14.58
Weighted-average exercise price, ending balance	8.85	$ 10.12
Weighted-average exercise price, options exercisable	$ 11.22
Average remaining contractual life	7 years 7 months 6 days	7 years 9 months 18 days
Average remaining contractual life, options exercisable	6 years 1 month 6 days
Aggregate intrinsic value	$ 3,143	$ 3,251
Aggregate intrinsic value, options exercisable	$ 2,240

Stock-Based Awards - Summary of Stock-Based Compensation Expense Related To Stock Options And Restricted Common Stock (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	$ 9,627	$ 8,301	$ 9,933
Research and Development [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	5,476	4,138	3,543
General and Administrative [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	$ 4,151	$ 4,163	$ 6,390

Net Loss Per Share - Computation of Basic and Diluted Earnings Per Share (Detail) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Numerator:
Net loss									$ (61,368)	$ (52,028)	$ (57,878)
Denominator:
Weighted average common shares outstanding, basic and diluted	37,036,065	36,619,575	27,565,064	27,541,594	27,489,397	27,483,550	27,407,408	27,350,673	32,228,721	27,433,239	27,297,934
Net loss per share, basic and diluted	$ (0.39)	$ (0.41)	$ (0.57)	$ (0.58)	$ (0.48)	$ (0.46)	$ (0.49)	$ (0.48)	$ (1.90)	$ (1.90)	$ (2.12)

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References + Details

Net Loss Per Share - Summary of Common Stock Equivalents Outstanding (Detail) - shares	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Options to Purchase Common Stock [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	5,024,371	4,494,201	3,115,003

Commitments and Contingencies - Additional Information (Detail)					12 Months Ended			18 Months Ended
	Jan. 01, 2017 ft²	Oct. 01, 2015	Apr. 15, 2015 Option	Jul. 28, 2014	Dec. 31, 2018 USD ($)	Dec. 31, 2017 USD ($)	Dec. 31, 2016 USD ($)	Jun. 30, 2020 USD ($)
Other Commitments [Line Items]
Operating lease, rental expense					$ 400,000	$ 300,000	$ 400,000
Subsequent Licensed Product [Member]
Other Commitments [Line Items]
Licensing fees per product maximum					1,300,000
Development Based Milestones [Member]
Other Commitments [Line Items]
Milestone payments due					0	$ 0	$ 0
Maximum [Member] \| Pre Commercialization Milestones [Member]
Other Commitments [Line Items]
Milestone payments					12,300,000
Maximum [Member] \| Product Commercialization Milestones [Member]
Other Commitments [Line Items]
Milestone payments					$ 12,500,000
Boston Office Space [Member]
Other Commitments [Line Items]
Lease expiration date				Jul. 31, 2020	Jul. 31, 2020
Boston Office Space [Member] \| Unrelated Third Party [Member]
Other Commitments [Line Items]
Subleased area \| ft²	2,976
Sublease expiration date	Jun. 30, 2020
Boston Office Space [Member] \| Unrelated Third Party [Member] \| Scenario Forecast [Member]
Other Commitments [Line Items]
Sublease rental income								$ 200,000
Additional Boston Office Space [Member]
Other Commitments [Line Items]
Lease expiration date			Jul. 31, 2020		Jul. 31, 2020
Lease extension period			3 years
Number of options to extend lease \| Option			1
San Diego Office Space [Member]
Other Commitments [Line Items]
Lease expiration date		Sep. 30, 2019
Lease extension period		5 years

Commitments and Contingencies - Schedule of Future Minimum Lease Payments for Operating Leases (Detail) $ in Thousands	Dec. 31, 2018 USD ($)
Commitments And Contingencies Disclosure [Abstract]
2019	$ 464
2020	226
2021	0
2022	0
Total	$ 690

Income Taxes - Additional Information (Detail) - USD ($)	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Income Taxes Disclosure [Line Items]
Income tax benefit	$ 0	$ 0	$ 0
Operating loss carryforwards, federal	16,600,000
Operating loss carry forwards, state	3,400,000
Uncertain tax position	0
Gross deferred tax assets	101,692,000	87,681,000
Unrecognized tax benefits	$ 0	$ 0
Federal statutory income tax rate	21.00%	34.00%	34.00%
Tax cuts and jobs act of 2017, net operating losses carryforward, maximum percentage of taxable income	80.00%
Tax Cuts and Jobs Act, Incomplete Accounting, Change in Tax Rate, Deferred Tax Liability, Provisional Income Tax Benefit		$ 33,800,000
Tax Cuts and Jobs Act, Change made to provision amount recognized in 2017 Tax Rate, Income Tax Expense (Benefit)	$ 0
Maximum [Member]
Income Taxes Disclosure [Line Items]
Federal statutory income tax rate		35.00%
No Expiration [Member]
Income Taxes Disclosure [Line Items]
Net operating loss carryforwards	9,500,000
Domestic Tax Authority [Member]
Income Taxes Disclosure [Line Items]
Net operating loss carryforwards	$ 55,700,000
Net operating loss carryforwards, beginning of expiration period	2026
Research and development tax credit carry forwards, beginning of expiration period	2026
State and Local Jurisdiction [Member]
Income Taxes Disclosure [Line Items]
Net operating loss carryforwards	$ 48,000,000
Net operating loss carryforwards, beginning of expiration period	2030
Research and development tax credit carry forwards, beginning of expiration period	2022

Income Taxes - Schedule of Domestic and Foreign Components of Loss Before Income Taxes (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Income Tax Disclosure [Abstract]
Domestic	$ (58,708)	$ (49,954)	$ (57,799)
Foreign	(2,660)	(2,074)	(79)
Loss before income taxes	$ (61,368)	$ (52,028)	$ (57,878)

Income Taxes - Reconciliation of Federal Statutory Income Tax Rate (Detail)	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Income Tax Disclosure [Abstract]
Federal statutory income tax rate	(21.00%)	(34.00%)	(34.00%)
Federal and state research and development tax credit	(4.20%)	(4.10%)	(2.90%)
State taxes, net of federal benefit	(3.70%)	(2.40%)	(3.90%)
Orphan drug tax credit	0.00%	0.00%	(1.30%)
Stock compensation expense	5.10%	1.50%	0.70%
Nondeductible Australia research and development expenses	0.90%	1.40%	(0.00%)
Impact of federal rate change related to tax reform	(0.00%)	65.20%	(0.00%)
Other items	(0.00%)	1.20%	1.30%
Change in deferred tax asset valuation allowance	22.90%	(28.80%)	40.10%
Effective income tax rate	0.00%	0.00%	0.00%

Income Taxes - Schedule of Net Deferred Tax Assets (Detail) - USD ($) $ in Thousands	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Noncurrent deferred tax assets:
Capitalized research and development expenses	$ 58,832	$ 49,325
Net operating loss carryforwards	16,728	13,848
Tax credit carryforwards	19,331	16,759
Capitalized legal expenses	1,918	1,646
Stock-based compensation	4,371	5,568
Accrued expenses	493	522
Other temporary differences	19	13
Total noncurrent deferred tax assets	101,692	87,681
Total gross deferred tax assets	101,692	87,681
Valuation allowance	(101,692)	(87,681)	$ (97,720)	$ (74,541)
Net deferred tax assets	$ 0	$ 0

Income Taxes - Summary of Changes in the Valuation Allowance for Deferred Tax Assets (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Income Tax Disclosure [Abstract]
Valuation allowance as of beginning of year	$ 87,681	$ 97,720	$ 74,541
Decreases recorded as benefit to income tax provision		(10,039)
Increases recorded to income tax provision	14,011		23,179
Valuation allowance as of end of year	$ 101,692	$ 87,681	$ 97,720

Retirement Plan - Additional Information (Detail) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Defined Contribution Plan Disclosure [Line Items]
Percentage of employer's contribution on employee's base salary	3.00%
Retirement 401K Plan [Member]
Defined Contribution Plan Disclosure [Line Items]
Contribution expense	$ 0.3
SIMPLE IRA plan [Member]
Defined Contribution Plan Disclosure [Line Items]
Contribution expense		$ 0.1	$ 0.2

Australia Research and Development Tax Incentive - Additional Information (Detail) - USD ($)	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Research and Development Tax Incentive [Line Items]
Unrealized foreign currency exchange (losses) gains	$ (76,000)	$ 46,000	$ (6,000)
Zafgen Australia Pty Limited [Member]
Research and Development Tax Incentive [Line Items]
Unrealized foreign currency exchange (losses) gains	(200,000)	100,000
Zafgen Australia Pty Limited [Member] \| Australia [Member]
Research and Development Tax Incentive [Line Items]
Tax incentive receivable	$ 1,500,000	900,000
Zafgen Australia Pty Limited [Member] \| Maximum [Member]
Research and Development Tax Incentive [Line Items]
Unrealized foreign currency exchange (losses) gains			(100,000)
Research and Development [Member] \| Zafgen Australia Pty Limited [Member]
Research and Development Tax Incentive [Line Items]
Percentage of refundable tax incentive	43.50%
Reduction to research and development expenses	$ 1,600,000	$ 900,000	$ 300,000
Percentage of reduction in research and development costs	43.50%	43.50%	45.00%

Restructuring - Additional Information (Detail) - USD ($) $ in Millions	1 Months Ended	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2016
Restructuring And Related Activities [Abstract]
Percentage of workforce reduction	31.00%
Restructuring charges		$ 1.4
Stock option modification non cash expense		$ 0.2

Restructuring - Summary of Restructuring Costs by Category (Detail) $ in Thousands	12 Months Ended
	Dec. 31, 2016 USD ($)
Restructuring Reserve Disclosures [Abstract]
Restructuring costs	$ 1,403
Research and Development [Member]
Restructuring Reserve Disclosures [Abstract]
Restructuring costs	462
General and Administrative [Member]
Restructuring Reserve Disclosures [Abstract]
Restructuring costs	941
Cash [Member]
Restructuring Reserve Disclosures [Abstract]
Restructuring costs	1,223
Cash [Member] \| Research and Development [Member]
Restructuring Reserve Disclosures [Abstract]
Restructuring costs	455
Cash [Member] \| General and Administrative [Member]
Restructuring Reserve Disclosures [Abstract]
Restructuring costs	768
Non-Cash [Member]
Restructuring Reserve Disclosures [Abstract]
Restructuring costs	180
Non-Cash [Member] \| Research and Development [Member]
Restructuring Reserve Disclosures [Abstract]
Restructuring costs	7
Non-Cash [Member] \| General and Administrative [Member]
Restructuring Reserve Disclosures [Abstract]
Restructuring costs	$ 173

Restructuring - Summary of Restructuring Reserve (Detail) $ in Thousands	12 Months Ended
	Dec. 31, 2017 USD ($)
Restructuring Reserve [Abstract]
Restructuring reserve beginning balance	$ 376
Restructuring expenses incurred during the period	24
Amounts paid during the period	$ (400)

Quarterly Financial Data - Schedule of Unaudited Consolidated Financial Statements (Detail) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
Quarterly Financial Information Disclosure [Abstract]
Revenue	$ 0	$ 0	$ 0	$ 0	$ 0	$ 0	$ 0	$ 0	$ 0	$ 0	$ 0
Operating expenses	14,691	15,169	15,560	15,702	13,358	12,840	13,536	13,265	$ 61,122	$ 52,999	$ 58,225
Net loss	$ (14,570)	$ (15,067)	$ (15,775)	$ (15,956)	$ (13,085)	$ (12,585)	$ (13,347)	$ (13,011)
Net loss per share, basic and diluted	$ (0.39)	$ (0.41)	$ (0.57)	$ (0.58)	$ (0.48)	$ (0.46)	$ (0.49)	$ (0.48)	$ (1.90)	$ (1.90)	$ (2.12)
Weighted average common shares outstanding, basic and diluted	37,036,065	36,619,575	27,565,064	27,541,594	27,489,397	27,483,550	27,407,408	27,350,673	32,228,721	27,433,239	27,297,934

Subsequent Events - Additional Information (Detail) - Subsequent Event [Member] - Center Plaza, Boston [Member] - Massachusetts [Member] - Shigo Center Plaza Owners LLC [Member] $ in Millions	Feb. 12, 2019 USD ($) ft²
Subsequent Event [Line Items]
Operating lease commencement date	Feb. 12, 2019
Area of office space \| ft²	17,705
Operating lease term	124 months
Lease extension period	60 months
Letter of credit \| $	$ 1.3

Subsequent Events - Schedule of Monthly Base Rent (Detail) - Subsequent Event [Member]	Feb. 12, 2019 USD ($)
Subsequent Event [Line Items]
Lease Year 1	$ 82,623
Lease Year 2	84,099
Lease Year 3	85,574
Lease Year 4	87,050
Lease Year 5	88,525
Lease Year 6	90,000
Lease Year 7	91,476
Lease Year 8	92,951
Lease Year 9	94,427
Lease Year 10	$ 95,902