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Document and Entity Information - shares	3 Months Ended
Document and Entity Information - shares	Mar. 31, 2020	Apr. 30, 2020
Cover [Abstract]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Mar. 31, 2020
Document Fiscal Year Focus	2020
Document Fiscal Period Focus	Q1
Entity Registrant Name	ZAFGEN, INC.
Entity Central Index Key	0001374690
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Interactive Data Current	Yes
Entity Filer Category	Non-accelerated Filer
Entity Small Business	true
Entity Emerging Growth Company	false
Entity Shell Company	false
Entity Common Stock, Shares Outstanding		37,469,596
Entity File Number	001-36510
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	20-3857670
Entity Address, Address Line One	3 Center Plaza
Entity Address, Address Line Two	Suite 610
Entity Address, City or Town	Boston
Entity Address, State or Province	MA
Entity Address, Postal Zip Code	02108
City Area Code	617
Local Phone Number	622-4003
Document Quarterly Report	true
Document Transition Report	false
Title of 12(b) Security	Common Stock
Trading Symbol	ZFGN
Security Exchange Name	NASDAQ

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Mar. 31, 2020	Dec. 31, 2019
Current assets:
Cash and cash equivalents	$ 38,980	$ 27,211
Marketable debt securities	24,905	43,050
Tax incentive receivable	214	243
Prepaid expenses and other current assets	581	999
Total current assets	64,680	71,503
Property and equipment, net	743	821
Operating lease right-of-use assets	6,928	7,051
Restricted cash	1,339	1,339
Other assets	12	20
Total assets	73,702	80,734
Current liabilities:
Accounts payable	322	632
Accrued expenses	881	1,190
Accrued restructuring costs	981	2,709
Operating lease liabilities, current	410	386
Notes payable, current	7,273	7,273
Total current liabilities	9,867	12,190
Notes payable, long-term	6,747	8,464
Operating lease liabilities	6,346	6,456
Total liabilities	22,960	27,110
Commitments and contingencies (Note 7)
Stockholders' equity:
Preferred stock; $0.001 par value per share; 5,000,000 shares authorized as of March 31, 2020 and December 31, 2019; no shares issued and outstanding as of March 31, 2020 and December 31, 2019
Common stock, $0.001 par value per share; 115,000,000 shares authorized as of March 31, 2020 and December 31, 2019; 37,469,596 and 37,446,498 shares issued and outstanding as of March 31, 2020 and December 31, 2019, respectively	37	37
Additional paid-in capital	450,623	449,903
Accumulated deficit	(399,949)	(396,351)
Accumulated other comprehensive income	31	35
Total stockholders' equity	50,742	53,624
Total liabilities and stockholders' equity	$ 73,702	$ 80,734

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Mar. 31, 2020	Dec. 31, 2019
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	37,469,596	37,446,498
Common stock, shares outstanding	37,469,596	37,446,498

Condensed Consolidated Statements of Operations and Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
Income Statement [Abstract]
Revenue	$ 0	$ 0
Operating expenses:
Research and development	(94)	9,631
General and administrative	3,647	3,646
Restructuring charges	10
Total operating expenses	3,563	13,277
Loss from operations	(3,563)	(13,277)
Other income (expense):
Interest income	258	642
Interest expense	(301)	(500)
Other income	218
Foreign currency transaction (losses) gains, net	(210)	23
Total other (expense) income, net	(35)	165
Net loss	$ (3,598)	$ (13,112)
Net loss per share, basic and diluted	$ (0.10)	$ (0.35)
Weighted average common shares outstanding, basic and diluted	37,467,411	37,313,947
Comprehensive loss:
Net loss	$ (3,598)	$ (13,112)
Other comprehensive (loss) income:
Unrealized (loss) gain on marketable debt securities	(4)	34
Total other comprehensive (loss) income	(4)	34
Total comprehensive loss	$ (3,602)	$ (13,078)

Condensed 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, 2018	$ 93,271	$ 37	$ 444,212	$ (350,945)	$ (33)
Beginning balance, shares at Dec. 31, 2018		37,287,221
Issuance of common stock upon exercise of stock options and employee stock purchase plan	95		95
Issuance of common stock upon exercise of stock options and employee stock purchase plan, shares		31,391
Issuance of restricted stock units, shares		4,467
Stock-based compensation expense	2,076		2,076
Unrealized gain (loss) on marketable debt securities	34				34
Net loss	(13,112)			(13,112)
Ending balance at Mar. 31, 2019	82,364	$ 37	446,383	(364,057)	1
Ending balance, shares at Mar. 31, 2019		37,323,079
Beginning balance at Dec. 31, 2019	53,624	$ 37	449,903	(396,351)	35
Beginning balance, shares at Dec. 31, 2019		37,446,498
Issuance of common stock upon exercise of stock options and employee stock purchase plan	10		10
Issuance of common stock upon exercise of stock options and employee stock purchase plan, shares		10,911
Issuance of restricted stock units, shares		12,187
Stock-based compensation expense	710		710
Unrealized gain (loss) on marketable debt securities	(4)				(4)
Net loss	(3,598)			(3,598)
Ending balance at Mar. 31, 2020	$ 50,742	$ 37	$ 450,623	$ (399,949)	$ 31
Ending balance, shares at Mar. 31, 2020		37,469,596

- Definition

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

+ References + Details

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
Cash flows from operating activities:
Net loss	$ (3,598)	$ (13,112)
Adjustments to reconcile net loss to net cash used in operating activities
Stock-based compensation expense	710	2,076
Depreciation expense	76	51
Loss on disposal of fixed assets	2
Unrealized foreign currency transaction losses (gains)	29	(14)
Amortization of discount on marketable debt securities	(52)	(283)
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	418	469
Tax incentive receivable		(94)
Accounts payable	(310)	(445)
Accrued restructuring costs	(1,728)
Accrued expenses	(163)	(1,119)
Net cash used in operating activities	(4,616)	(12,471)
Cash flows from investing activities:
Proceeds from sales and maturities of marketable debt securities	20,532	34,275
Purchases of marketable debt securities	(2,339)	(33,466)
Purchases of property and equipment		(2)
Net cash provided by investing activities	18,193	807
Cash flows from financing activities:
Repayment of notes payable	(1,818)
Proceeds from exercise of common stock options and employee stock purchase plan	10	95
Net cash (used in) provided by financing activities	(1,808)	95
Net increase (decrease) in cash, cash equivalents and restricted cash	11,769	(11,569)
Cash, cash equivalents and restricted cash at beginning of period	28,550	49,331
Cash, cash equivalents and restricted cash at end of period	40,319	37,762
Supplemental disclosure of non-cash investing and financing activities:
Property and equipment included in accounts payable		11
Supplemental disclosure of cash flow information:
Cash paid for interest	$ 212	$ 339

Nature of the Business and Basis of Presentation

3 Months Ended

Mar. 31, 2020

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 biopharmaceutical company that has leveraged its proprietary knowledge of the methionine aminopeptidase 2 (“MetAP2”) pathway to pioneer the study of MetAP2 inhibitors in both common and rare metabolic disorders.

Following an extensive process of evaluating strategic alternatives for the Company and identifying and reviewing potential candidates for a strategic acquisition or other transaction, on December 17, 2019, the Company entered into an Agreement and Plan of Merger, or the Merger Agreement, with Chondrial Therapeutics, Inc., or Chondrial, pursuant to which a wholly owned subsidiary of the Company will merge with and into Chondrial, with Chondrial continuing as the surviving corporation of the merger and a wholly owned subsidiary of the Company, or the merger. Under the exchange ratio formula in the Merger Agreement, as of immediately after the merger, the former Chondrial securityholders are expected to own approximately 60% of the outstanding shares of the Company’s common stock on a fully-diluted basis and the Company’s stockholders as of immediately prior to the merger are expected to own approximately 40% of the outstanding shares of the Company’s common stock on a fully-diluted basis. The relative percentage ownership of the combined company was derived using a stipulated value of Chondrial of approximately $67.5 million and of the Company of approximately $45.0 million. The Company’s valuation was determined based on a projected net cash, cash equivalents and marketable securities balance minus outstanding liabilities, as defined in the Merger Agreement, of $40.0 million as of a determination date prior to the closing of the merger, but subject to adjustment as described below, plus an additional $5.0 million of enterprise value. If the Company’s actual net cash is between $39.5 million and $40.5 million, no adjustment will be made to the ownership percentages based on the Company’s net cash. The Company’s target net cash, lower target net cash and upper target net cash amounts will be reduced by $21,311 per day beginning on March 31, 2020 through the closing date of the merger, and the Chondrial valuation will be increased by $111,656 per day beginning on March 31, 2020 through the closing date of the merger, resulting in a corresponding adjustment to the exchange ratio and an increase to the ownership percentage of Chondrial’s stockholder in the combined company.

The Merger Agreement provides the Company and Chondrial with specified termination rights, and further provides that, upon termination of the Merger Agreement under specified circumstances, either party may be required to pay the other party a termination fee of $3,375,000. In addition, in connection with certain terminations of the Merger Agreement, either party may be required to pay the other party’s third party expenses up to $350,000. In connection with the merger, the Company will seek to amend its certificate of incorporation to: (i) effect a reverse split of the Company’s common stock at a ratio to be determined by the Company and Chondrial, which is intended to ensure that the listing requirements of the Nasdaq Global Market are satisfied and (ii) change the name of Zafgen, Inc. to “Larimar Therapeutics, Inc.”

The Company’s and Chondrial’s obligations to consummate the merger are subject to the satisfaction or waiver of customary closing conditions, including, among others, obtaining the requisite approvals of the Company’s stockholders and satisfaction of minimum net cash thresholds of $30,000,000 by the Company and not less than zero by Chondrial. The sole stockholder of Chondrial has approved the Merger Agreement. In connection with the execution of the Merger Agreement, the Company entered into stockholder support agreements with its current directors and certain officers and the Company’s largest stockholder, which collectively beneficially own or control an aggregate of approximately 9.7% of its outstanding shares of common stock. Each of the stockholders party to such stockholder support agreements has agreed to vote or cause to be voted, all of the shares of the Company’s common stock beneficially owned by such stockholder in favor of the stockholder proposals submitted at the Company’s stockholders meeting to be held in connection with the merger.

The Company expects to devote significant time and resources to the completion of the merger with Chondrial. However, there can be no assurance that such activities will result in the completion of the merger. Further, the completion of the merger ultimately may not deliver the anticipated benefits or enhance shareholder value.

The Company has incurred losses and negative cash flows from operations since its inception. As of March 31, 2020, the Company had an accumulated deficit of $399.9 million. From its inception through March 31, 2020, 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 5 to the condensed consolidated financial statements, the Company has a term loan with an aggregate principal balance of $12.7 million as of March 31, 2020 The loan agreement requires that the Company maintain certain minimum liquidity at all times, which as of March 31, 2020 was approximately $13.4 million. If the minimum liquidity covenant is not met, the Company may be required to repay the loan prior to scheduled maturity dates. 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 amounts due under the Term Loan. 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. During the quarter ended March 31, 2020 the Company was in compliance with all covenants under the term loan. The Company has estimated that the risk of subjective acceleration under the Term Loan’s material adverse events clause is reasonably possible, however not probable and therefore has classified the outstanding principal balance in current and long-term liabilities based on contractually scheduled principal payments. However, the assessment of such probability of the debt holder calling the debt is subjective and their actions and/or the Company’s related assessment could change in the future, which in turn would impact the classification of the debt balances.

Based on its current operating plans, the Company believes its cash, cash equivalents and marketable debt securities of $63.9 million as of March 31, 2020, 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 date of this Quarterly Report. 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. 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 future 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 ourselves.

On April 21, 2020, the Company received a deficiency letter from the Listing Qualifications Department of the Nasdaq Stock Market notifying it that, for the last 30 consecutive business days, the bid price for the Company’s common stock had closed below the minimum $1.00 per share requirement for continued inclusion on the Nasdaq Global Market, referred to as the minimum bid price rule. In accordance with Nasdaq Listing Rules, the Company has an initial period of 180 calendar days. On April 16, 2020, Nasdaq announced it was providing temporary relief from continued listing bid price requirements through June 30, 2020. Under the relief the Company will have additional time to regain compliance with the listing bid price requirements with the compliance period beginning July 1, 2020. As such, the compliance period for the Company will expire on December 28, 2020. The Company is actively monitoring its stock price and will consider any and all options available to the Company to maintain compliance. The alternatives to trading on the Nasdaq Capital Market or another national securities exchange are generally considered to be less efficient and less broad-based than the national securities exchanges and the liquidity of the Company’s common stock will likely be reduced if we fail to regain compliance with the minimum bid price rule.

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

Unaudited Interim Financial Information

The condensed consolidated balance sheet as of December 31, 2019 was derived from the Company’s audited financial statements, but does not include all disclosures required by accounting principles generally accepted in the United States of America (“GAAP”). The accompanying unaudited condensed consolidated financial statements as of March 31, 2020 and for the three months ended March 31, 2020 and 2019, have been prepared by the Company, pursuant to the rules and regulations of the Securities and Exchange Commission (“SEC”), for interim financial statements. Certain information and footnote disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted pursuant to such rules and regulations. However, the Company believes that the disclosures are adequate to make the information presented not misleading. These condensed consolidated financial statements should be read in conjunction with the Company’s audited consolidated financial statements and the notes thereto for the year ended December 31, 2019, included in the Company’s Annual Report on Form 10-K, for the year ended December 31, 2019, on file with the SEC. In the opinion of management, all adjustments, consisting only of normal recurring adjustments necessary for a fair statement of the Company’s condensed consolidated financial position as of March 31, 2020 and condensed consolidated results of operations and cash flows for the three months ended March 31, 2020 and 2019 have been made. The results of operations for the three months ended March 31, 2020 are not necessarily indicative of the results of operations that may be expected for the year ending December 31, 2020.

Summary of Significant Accounting Policies

3 Months Ended

Mar. 31, 2020

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 condensed consolidated financial statements, and the reported amounts of expenses during the reporting periods. Significant estimates and assumptions reflected in these condensed 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.

Marketable debt securities

Marketable debt securities consist of debt investments with original maturities greater than ninety days. The Company has classified its debt investments with maturities beyond one year as short term, based on their highly liquid nature and because such marketable debt securities represent the investment of cash that is available for current operations. The Company classifies its marketable debt securities as available-for-sale. Accordingly, these investments are recorded at fair value, which is based on quoted market prices. When the fair value is below the amortized cost the amount of the expected credit loss is estimated. The credit-related impairment amount is recognized in net income; the remaining impairment amount and unrealized gains are reported as a component of accumulated other comprehensive income in stockholders’ equity. Credit losses are recognized through the use of an allowance for credit losses account and subsequent improvements in expected credit losses are recognized as a reversal of the allowance account. If the Company has the intent to sell the security or it is more likely than not that the Company will be required to sell the security prior to recovery of its amortized cost basis, the allowance for credit loss is written off and the excess of the amortized cost basis of the asset over its fair value is recorded in net income.

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.

The Company excluded the following common stock equivalents, outstanding as of March 31, 2020 and 2019, from the computation of diluted net loss per share for the three months ended March 31, 2020 and 2019 because they had an anti-dilutive impact due to the net loss incurred for the periods:

	As of March 31,
	2020		2019
Options to purchase common stock		3,945,647		6,663,162
Unvested restricted common stock		40,766		351,371
		3,986,413		7,014,533

Risks and Uncertainties

The Company is subject to risks and uncertainties as a result of the COVID-19 pandemic. The extent of the impact of the COVID-19 pandemic on the Company's business is highly uncertain and difficult to predict, as the response to the pandemic is in its incipient stages and information is rapidly evolving. Capital markets and economies worldwide have also been negatively impacted by the COVID-19 pandemic, and it is possible that it could cause a local and/or global economic recession. Such economic disruption could have a material adverse effect on the Company’s business. Policymakers around the globe have responded with fiscal policy actions to support the healthcare industry and economy as a whole. The magnitude and overall effectiveness of these actions remains uncertain.

The severity of the impact of the COVID-19 pandemic on the Company's business will depend on a number of factors, including, but not limited to, the duration and severity of the pandemic, all of which are uncertain and cannot be predicted. The Company is required to have a net cash balance of at least $30,000,000 at the closing of the merger as a condition to Chondrial’s obligation to consummate the merger. For purposes of the merger agreement, net cash is subject to certain reductions, including, without limitation, accounts payable, accrued expenses (except those related to the merger), current liabilities payable in cash, unpaid expenses related to the merger and certain other unpaid obligations, including outstanding lease obligations. The liability with regards to the Company’s outstanding lease obligations is a large component of the Company’s net cash and COVID-19 has created uncertainties surrounding our ability to take the steps necessary to sublease or negotiate a buy-out of our existing leases. In the event that the Company’s net cash falls below this threshold, a condition to the Chondrial’s obligation to consummate the merger will fail to be satisfied and Chondrial will have the right to terminate the merger agreement at an outside date of September 17, 2020 (subject to extension as provided in the merger agreement) if the Company’s net cash continues to be lower than the $30,000,000 threshold. As of the date of issuance of these condensed consolidated financial statements, the extent to which the COVID-19 pandemic may materially impact the Company's financial condition, liquidity, or results of operations is uncertain.

Recently Issued and Adopted Accounting Pronouncements

In June 2016 the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (“ASU”) No. 2016-13, Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments. The FASB subsequently issued amendments to ASU 2016-13, which have the same effective date and transition date of January 1, 2020. This standard requires entities to estimate an expected lifetime credit loss on financial assets ranging from short-term trade accounts receivable to long-term financings and report credit losses using an expected losses model rather than the incurred losses model that was previously used, and establishes additional disclosures related to credit risks. For available-for-sale debt securities with unrealized losses, the standard now requires allowances to be recorded instead of reducing the amortized cost of the investment. This standard limits the amount of credit losses to be recognized for available-for-sale debt securities to the amount by which carrying value exceeds fair value and requires the reversal of previously recognized credit losses if fair value increases.

This standard became effective for the Company on January 1, 2020, and based on the composition of the Company’s marketable debt securities, current economic conditions and historical credit loss activity, the adoption of this standard did not have a material impact on the Company’s condensed consolidated financial statements and related disclosures.

In August 2018 the FASB issued ASU No. 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework - Changes to the Disclosure Requirements for Fair Value Measurement. This standard modifies certain disclosure requirements on fair value measurements. This standard became effective for the Company on January 1, 2020. The adoption of this standard did not have a material impact on the Company’s disclosures.

Fair Value Measurements and Marketable Debt Securities

3 Months Ended

Mar. 31, 2020

Fair Value Disclosures [Abstract]

Fair Value Measurements and Marketable Debt Securities

3. Fair Value Measurements and Marketable Debt Securities

Fair Value Measurements

The following tables present information about the Company’s financial assets that have been measured at fair value as of March 31, 2020 and December 31, 2019 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.

The following tables summarize the Company’s cash equivalents and marketable debt securities as of March 31, 2020 and December 31, 2019:

	March 31, 2020
			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	$	35,865	$	35,865	$	—	$	—
Total cash equivalents		35,865		35,865		—		—

Marketable debt securities:
U.S. government securities		10,629		—		10,629		—
Corporate bonds		8,589		—		8,589		—
Commercial paper		5,687		—		5,687		—
Total marketable debt securities		24,905		—		24,905		—
Total cash equivalents and marketable debt securities	$	60,770	$	35,865	$	24,905	$	—

		December 31, 2019
				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		$	18,289	$	18,289	$	—	$	—
U.S. Government securities			3,098		—		3,098		—
Commercial paper			1,047		—		1,047		—
Total cash equivalents			22,434		18,289		4,145		—

Marketable debt securities:
U.S. Government securities			14,996		—		14,996		—
Corporate bonds			14,648		—		14,648		—
Commercial paper			13,406		—		13,406		—
Total marketable debt securities			43,050		—		43,050		—
Total cash equivalents and marketable debt securities		$	65,484	$	18,289	$	47,195	$	—

The carrying amounts reflected in the condensed 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 Debt Securities

The following tables summarize the Company’s marketable debt securities as of March 31, 2020 and December 31, 2019:

	March 31, 2020
			Gross		Gross
	Amortized		Unrealized		Unrealized
	Cost		Gains		Losses			Fair Value
	(in thousands)
Assets:
U.S. government securities (due within 1 year)	$	10,596	$	33	$	—		$	10,629
Corporate bonds (due within 1 year)		8,590		3		(4	)		8,589
Commercial paper (due within 1 year)		5,687		—		—			5,687
	$	24,873	$	36	$	(4	)	$	24,905

As of March 31, 2020, the Company did not have an allowance for credit losses.

	December 31, 2019
			Gross		Gross
	Amortized		Unrealized		Unrealized
	Cost		Gains		Losses		Fair Value
	(in thousands)
Assets:
U.S. Government securities (due within 1 year)	$	14,981	$	15	$	—	$	14,996
Corporate bonds (due within 1 year)		14,628		20		—		14,648
Commercial paper (due within 1 year)		13,406		—		—		13,406
	$	43,015	$	35	$	—	$	43,050

- 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

Accrued Expenses

3 Months Ended

Mar. 31, 2020

Payables And Accruals [Abstract]

Accrued Expenses

4. Accrued Expenses

Accrued expenses consisted of the following as of March 31, 2020 and December 31, 2019:

	March 31,		December 31,
	2020		2019
	(in thousands)
Accrued payroll and related expenses	$	193	$	37
Accrued professional fees		452		864
Accrued other		236		289
	$	881	$	1,190

Notes Payable

3 Months Ended

Mar. 31, 2020

Debt Disclosure [Abstract]

Notes Payable

5. 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 the Term Loan, the Company became 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 interest at an annual rate of 1.25% above the prime rate, which at March 31, 2020 was 3.25%. 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.

Additionally, the Company, as borrower, is required to maintain a minimum cash, cash equivalents and marketable debt securities balance at Silicon Valley Bank of no less than 105% of the total outstanding principal balance of the Term Loan, which was $13.4 million as of March 31, 2020 and $15.3 million as of December 31, 2019.

Further, since 45 days after the Term Loan was entered in, the Company has met its obligation to maintain a balance of unrestricted cash, cash equivalents and marketable debt 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 Debt 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; limiting 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 amounts due 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 March 31, 2020 and December 31, 2019, notes payable consist of the following:

	March 31,			December 31,
	2020			2019
	(in thousands)
Notes payable	$	12,728		$	14,545
Less: current portion		(7,273	)		(7,273	)
Notes payable, net of current portion		5,455			7,272
Accretion related to final payment		1,292			1,192
Notes payable, long term	$	6,747		$	8,464

During the three months ended March 31, 2020 and 2019, the Company recognized $0.3 million and $0.5 million of interest expense, respectively, related to the Term Loan. The effective annual interest rate as of March 31, 2020 on the outstanding debt under the Term Loan was approximately 7.7%.

Stock-Based Awards

3 Months Ended

Mar. 31, 2020

Disclosure Of Compensation Related Costs Sharebased Payments [Abstract]

Stock-Based Awards

6. Stock-Based Awards

The Company’s 2014 Stock Option and Incentive Plan, as amended (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 Company has outstanding stock-based awards under its Amended and Restated 2006 Stock Option Plan but is no longer granting awards under this plan. The Company also issues common stock under its 2014 Employee Stock Purchase Plan (the “ESPP”). As of March 31, 2020, 6,795,572 shares are available for grant under the 2014 Plan, including 1,497,859 shares automatically added to the 2014 Plan on January 1, 2020, and 58,611 shares are available for issuance to participating employees under the ESPP.

The Company recorded stock-based compensation expense related to stock options, restricted common stock and the ESPP in the following expense categories within its condensed consolidated statements of operations for the three months ended March 31, 2020 and 2019 as follows:

	Three Months Ended March 31,
	2020			2019
	(in thousands)
Research and development	$	(144	)	$	960
General and administrative		854			1,116
	$	710		$	2,076

The Company recorded negative research and development expenses during the three months ended March 31, 2020, which was the result of the reversal of related stock compensation expense related to the termination of the Company’s final research and development employee in the first quarter of 2020.

Commitments and Contingencies

3 Months Ended

Mar. 31, 2020

Commitments And Contingencies Disclosure [Abstract]

Commitments and Contingencies

7. Commitments and Contingencies

Leases

On February 12, 2019, the Company entered into a lease with Shigo Center Plaza Owners, LLC, for approximately 17,705 square feet of office space for a new headquarters located at 3 Center Plaza, Boston, Massachusetts. The lease has a term of 124 months with an option to extend the 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 and is classified as restricted cash within the consolidated financial statements. Under the lease agreement, the Company began paying monthly rent beginning four months after the lease commencement, which was June 21, 2019, with total lease payments over the initial term of $10.7 million. During the fourth quarter of 2019 and in conjunction with entering into the Merger Agreement with Chondrial, the Company performed an impairment review of the Company’s headquarters lease and related assets and determined that an impairment had not occurred as the estimated fair value of the asset exceeded the carrying value. In addition, due to the continued impact of the COVID-19 pandemic, the Company updated its impairment review as of March 31, 2020 and determined that an impairment had not occurred.

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 extended to expire on December 31, 2024.

The future minimum lease payments for the next five years and thereafter as of March 31, 2020, are as follows:

Year Ending December 31,	Operating
(in thousands)	Leases
2020 (April - December)		824
2021		1,120
2022		1,143
2023		1,165
2024		1,189
Thereafter		5,396
Total lease payments		10,837
Less: imputed interest		(4,081	)
Present value of lease liabilities	$	6,756

During the three months ended March 31, 2020 the Company did not incur any lease expense associated with research and development activities, and the Company incurred $0.3 million of lease expense associated with general and administrative activities. During the three months ended March 31, 2019 the Company incurred $0.1 million of lease expense associated with research and development activities and less than $0.1 million of lease expense associated with general and administrative activities. The components of lease expense are as follows:

	Three Months Ended March 31,
	2020			2019
	(in thousands)
Operating lease cost	$	331		$	127
Short-term lease cost		—			41
Sublease income		(28	)		(28	)
Total lease cost	$	303		$	140

The weighted average remaining lease term and weighted average discount rate of our operating leases are as follows:

	As of March 31,			As of December 31,
	2020			2019
Weighted average remaining lease term in years		9.24			9.49
Weighted average discount rate		11.1	%		11.1	%

Cash paid for amounts included in the measurement of operating lease liabilities was $0.3 million and $0.1 million during the three months ended March 31, 2020 and 2019, respectively, and is included in operating activities within the condensed consolidated statements of cash flows. There were no additional right-of-use assets recognized as non-cash asset additions that resulted from new operating lease liabilities during the three months ended March 31, 2020 or 2019.

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 its management team and its board of directors 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 condensed consolidated financial statements as of March 31, 2020.

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. The Company is not aware of any material claims as of March 31, 2020.

Retirement Plan

3 Months Ended

Mar. 31, 2020

Compensation And Retirement Disclosure [Abstract]

Retirement Plan

8. 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 full-time employees.

During the three months ended March 31, 2020 and 2019, the Company recognized less than $0.1 million and $0.1 million, respectively, of expense related to its contributions to the 401(k) plan.

Australia Research and Development Tax Incentive

3 Months Ended

Mar. 31, 2020

Research And Development [Abstract]

Australia Research and Development Tax Incentive

9. 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 three months ended March 31, 2019, $0.1 million was recorded as a reduction to research and development expenses in the condensed consolidated statements of operations. This amount represented 43.5% of the Company’s qualified research and development spending in Australia. For the three months ended March 31, 2020, the Company did not have qualified research and development expenses. 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 three months ended March 31, 2020 and 2019, the Company recorded in its condensed consolidated statements of operations unrealized foreign currency exchange losses of $0.2 million and gains of less than $0.1 million, respectively, related to this tax incentive receivable. As of March 31, 2020 and December 31, 2019, the Company’s tax incentive receivable from the Australian government was $0.2 million.

Restructuring

3 Months Ended

Mar. 31, 2020

Restructuring And Related Activities [Abstract]

Restructuring

10. Restructuring

In September 2019, the Company’s Board of Directors approved a restructuring plan to reduce operating costs and better align the Company’s workforce with the needs of its business following the Company’s September 5, 2019 announcement regarding the low probability of resolving the clinical hold of ZGN-1061 in the near-term and that the Company will be seeking strategic alternatives.

Under the restructuring plan and a previously announced July 2019 restructuring, the Company reduced its workforce by 20 employees and closed its office in San Diego, California. Affected employees are eligible to receive severance payments and outplacement services in connection with the reduction. In the three months ended March 31, 2020, the Company recorded aggregate restructuring charges of less than $0.1 million related to other employee-related costs. The Company does not expect to incur any additional significant costs associated with these restructurings. During the three months ended March 31, 2020, $1.7 million of the estimated restructuring charges were paid. The Company expects the remaining accrued restructuring costs of $1.0 million will be paid in the next 12 months.

The following table shows the total amount expected to be incurred and the liability related to the 2019 restructuring as of March 31, 2020:

	One-Time
	Employee			Contract
	Termination			Termination			Total
	Benefits			Costs			Expenses
	(in thousands)
Accrued restructuring costs as of December 31, 2019	$	2,706		$	3		$	2,709
Restructuring charges incurred during the period		10			—			10
Amounts paid during the period		(1,735	)		(3	)		(1,738	)
Accrued restructuring costs as of March 31, 2020	$	981		$	—		$	981

The following table summarizes the restructuring charges by category for the period ending March 31, 2020:

	Three Months Ended March 31, 2020
	(in thousands)
	Cash		Non-Cash		Total
Research and development	$	10	$	—	$	10
General and administrative		—		—		—
	$	10	$	—	$	10

Summary of Significant Accounting Policies (Policies)

3 Months Ended

Mar. 31, 2020

Accounting Policies [Abstract]

Use of Estimates

Marketable Debt Securities

Marketable debt securities

Net Loss Per Share

	As of March 31,
	2020		2019
Options to purchase common stock		3,945,647		6,663,162
Unvested restricted common stock		40,766		351,371
		3,986,413		7,014,533

Risks and Uncertainties

Recently Issued and Adopted Accounting Pronouncements

Summary of Significant Accounting Policies (Tables)

3 Months Ended

Mar. 31, 2020

Accounting Policies [Abstract]

Summary of Common Stock Equivalents Outstanding

	As of March 31,
	2020		2019
Options to purchase common stock		3,945,647		6,663,162
Unvested restricted common stock		40,766		351,371
		3,986,413		7,014,533

Fair Value Measurements and Marketable Debt Securities (Tables)

3 Months Ended

Mar. 31, 2020

Fair Value Disclosures [Abstract]

Summary of Cash Equivalents and Marketable Debt Securities

The following tables summarize the Company’s cash equivalents and marketable debt securities as of March 31, 2020 and December 31, 2019:

	March 31, 2020
			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	$	35,865	$	35,865	$	—	$	—
Total cash equivalents		35,865		35,865		—		—

Marketable debt securities:
U.S. government securities		10,629		—		10,629		—
Corporate bonds		8,589		—		8,589		—
Commercial paper		5,687		—		5,687		—
Total marketable debt securities		24,905		—		24,905		—
Total cash equivalents and marketable debt securities	$	60,770	$	35,865	$	24,905	$	—

		December 31, 2019
				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		$	18,289	$	18,289	$	—	$	—
U.S. Government securities			3,098		—		3,098		—
Commercial paper			1,047		—		1,047		—
Total cash equivalents			22,434		18,289		4,145		—

Marketable debt securities:
U.S. Government securities			14,996		—		14,996		—
Corporate bonds			14,648		—		14,648		—
Commercial paper			13,406		—		13,406		—
Total marketable debt securities			43,050		—		43,050		—
Total cash equivalents and marketable debt securities		$	65,484	$	18,289	$	47,195	$	—

Summary of Marketable Debt Securities

The following tables summarize the Company’s marketable debt securities as of March 31, 2020 and December 31, 2019:

	March 31, 2020
			Gross		Gross
	Amortized		Unrealized		Unrealized
	Cost		Gains		Losses			Fair Value
	(in thousands)
Assets:
U.S. government securities (due within 1 year)	$	10,596	$	33	$	—		$	10,629
Corporate bonds (due within 1 year)		8,590		3		(4	)		8,589
Commercial paper (due within 1 year)		5,687		—		—			5,687
	$	24,873	$	36	$	(4	)	$	24,905

	December 31, 2019
			Gross		Gross
	Amortized		Unrealized		Unrealized
	Cost		Gains		Losses		Fair Value
	(in thousands)
Assets:
U.S. Government securities (due within 1 year)	$	14,981	$	15	$	—	$	14,996
Corporate bonds (due within 1 year)		14,628		20		—		14,648
Commercial paper (due within 1 year)		13,406		—		—		13,406
	$	43,015	$	35	$	—	$	43,050

Accrued Expenses (Tables)

3 Months Ended

Mar. 31, 2020

Payables And Accruals [Abstract]

Schedule of Accrued Expenses

Accrued expenses consisted of the following as of March 31, 2020 and December 31, 2019:

	March 31,		December 31,
	2020		2019
	(in thousands)
Accrued payroll and related expenses	$	193	$	37
Accrued professional fees		452		864
Accrued other		236		289
	$	881	$	1,190

Notes Payable (Tables)

3 Months Ended

Mar. 31, 2020

Debt Disclosure [Abstract]

Schedule of Notes Payable

As of March 31, 2020 and December 31, 2019, notes payable consist of the following:

	March 31,			December 31,
	2020			2019
	(in thousands)
Notes payable	$	12,728		$	14,545
Less: current portion		(7,273	)		(7,273	)
Notes payable, net of current portion		5,455			7,272
Accretion related to final payment		1,292			1,192
Notes payable, long term	$	6,747		$	8,464

Stock-Based Awards (Tables)

3 Months Ended

Mar. 31, 2020

Disclosure Of Compensation Related Costs Sharebased Payments [Abstract]

Summary of Stock-Based Compensation Expense Related to Stock Options, Restricted Common Stock and ESPP

	Three Months Ended March 31,
	2020			2019
	(in thousands)
Research and development	$	(144	)	$	960
General and administrative		854			1,116
	$	710		$	2,076

Commitments and Contingencies (Tables)

3 Months Ended

Mar. 31, 2020

Commitments And Contingencies Disclosure [Abstract]

Schedule of Future Minimum Lease Payments for Operating Leases

The future minimum lease payments for the next five years and thereafter as of March 31, 2020, are as follows:

Year Ending December 31,	Operating
(in thousands)	Leases
2020 (April - December)		824
2021		1,120
2022		1,143
2023		1,165
2024		1,189
Thereafter		5,396
Total lease payments		10,837
Less: imputed interest		(4,081	)
Present value of lease liabilities	$	6,756

Schedule of Components of Leases Expense

The components of lease expense are as follows:

	Three Months Ended March 31,
	2020			2019
	(in thousands)
Operating lease cost	$	331		$	127
Short-term lease cost		—			41
Sublease income		(28	)		(28	)
Total lease cost	$	303		$	140

Schedule of Weighted Average Remaining Lease Term and Weighted Average Discount Rate of Operating Leases

The weighted average remaining lease term and weighted average discount rate of our operating leases are as follows:

	As of March 31,			As of December 31,
	2020			2019
Weighted average remaining lease term in years		9.24			9.49
Weighted average discount rate		11.1	%		11.1	%

Restructuring (Tables)

3 Months Ended

Mar. 31, 2020

Restructuring And Related Activities [Abstract]

Summary of Accrued Restructuring Costs

The following table shows the total amount expected to be incurred and the liability related to the 2019 restructuring as of March 31, 2020:

	One-Time
	Employee			Contract
	Termination			Termination			Total
	Benefits			Costs			Expenses
	(in thousands)
Accrued restructuring costs as of December 31, 2019	$	2,706		$	3		$	2,709
Restructuring charges incurred during the period		10			—			10
Amounts paid during the period		(1,735	)		(3	)		(1,738	)
Accrued restructuring costs as of March 31, 2020	$	981		$	—		$	981

Summary of Restructuring Charges by Category

The following table summarizes the restructuring charges by category for the period ending March 31, 2020:

	Three Months Ended March 31, 2020
	(in thousands)
	Cash		Non-Cash		Total
Research and development	$	10	$	—	$	10
General and administrative		—		—		—
	$	10	$	—	$	10

Nature of the Business and Basis of Presentation - Additional Information (Detail) - USD ($)				3 Months Ended	173 Months Ended
	Mar. 31, 2020	Dec. 17, 2019	Jul. 02, 2018	Mar. 31, 2020	Mar. 31, 2020	Apr. 21, 2020	Dec. 31, 2019	Dec. 29, 2017
Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items]
Entity incorporation date				Nov. 22, 2005
Adjusted ownership value prior to closing merger		$ 40,000,000
Additional enterprise value		5,000,000
Cash valuation reduction	$ 21,311
Merger agreement minimum required net cash thresholds	30,000,000	$ 30,000,000		$ 30,000,000	$ 30,000,000
Accumulated deficit	399,949,000			399,949,000	399,949,000		$ 396,351,000
Net proceeds from sale of securities					397,900,000
Credit facility default amount	300,000			300,000	300,000
Total cash, cash equivalents and marketable securities	63,900,000			63,900,000	63,900,000
Term Loan [Member]
Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items]
Aggregate principal balance	12,700,000			12,700,000	12,700,000			$ 20,000,000
Loan agreement minimum liquidity required	13,400,000			13,400,000	13,400,000		$ 15,300,000
Credit facility default amount	300,000			300,000	300,000
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			$ 64,600,000
Maximum [Member]
Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items]
Net cash threshold	40,500,000			40,500,000	40,500,000
Minimum [Member]
Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items]
Net cash threshold	39,500,000			39,500,000	39,500,000
Minimum [Member] \| Subsequent Event [Member]
Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items]
Bid price of share as per rule						$ 1.00
Minimum [Member] \| Term Loan [Member]
Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items]
Total cash, cash equivalents and marketable securities	55,000,000			$ 55,000,000	$ 55,000,000
Chondrial Security Holders [Member]
Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items]
Percentage of expected diluted common shares immediately after merger		60.00%
Common stock, value immediately after merger		$ 67,500,000
Increase in valuation of ownership	$ 111,656
Company Stockholders Prior to Merger [Member]
Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items]
Percentage of expected diluted common shares immediately after merger		40.00%
Common stock, value immediately after merger		$ 45,000,000
Chondrial Therapeutics Inc. [Member]
Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items]
Date of merger agreement		Dec. 17, 2019
Merger agreement termination fee to be paid by either party to other party upon termination of agreement		$ 3,375,000
Merger agreement minimum required net cash thresholds		$ 0
Beneficiary interest percentage in outstanding common stock		9.70%
Chondrial Therapeutics Inc. [Member] \| Maximum [Member]
Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items]
Additional third party expenses to be paid by either party to other party upon termination of merger agreement		$ 350,000

Summary of Significant Accounting Policies - Summary of Common Stock Equivalents Outstanding (Detail) - shares	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	3,986,413	7,014,533
Options to Purchase Common Stock [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	3,945,647	6,663,162
Unvested Restricted Common Stock [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	40,766	351,371

Summary of Significant Accounting Policies - Additional Information (Detail) - USD ($)	Mar. 31, 2020	Dec. 17, 2019
Accounting Policies [Abstract]
Merger agreement minimum required net cash thresholds	$ 30,000,000	$ 30,000,000

Fair Value Measurements and Marketable Debt Securities - Summary of Cash Equivalents and Marketable Debt Securities (Detail) - USD ($) $ in Thousands	Mar. 31, 2020	Dec. 31, 2019
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	$ 35,865	$ 22,434
Marketable debt securities	24,905	43,050
Total cash equivalents and marketable debt securities	60,770	65,484
Money Market Funds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	35,865	18,289
U.S. Government Securities [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents		3,098
Marketable debt securities	10,629	14,996
Corporate Bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Marketable debt securities	8,589	14,648
Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents		1,047
Marketable debt securities	5,687	13,406
Quoted Prices in Active Markets, (Level 1) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	35,865	18,289
Total cash equivalents and marketable debt securities	35,865	18,289
Quoted Prices in Active Markets, (Level 1) [Member] \| Money Market Funds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	35,865	18,289
Significant Other Observable Inputs (Level 2) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents		4,145
Marketable debt securities	24,905	43,050
Total cash equivalents and marketable debt securities	24,905	47,195
Significant Other Observable Inputs (Level 2) [Member] \| U.S. Government Securities [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents		3,098
Marketable debt securities	10,629	14,996
Significant Other Observable Inputs (Level 2) [Member] \| Corporate Bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Marketable debt securities	8,589	14,648
Significant Other Observable Inputs (Level 2) [Member] \| Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents		1,047
Marketable debt securities	$ 5,687	$ 13,406

Fair Value Measurements and Marketable Debt Securities - Summary of Marketable Debt Securities (Detail) - USD ($) $ in Thousands	Mar. 31, 2020	Dec. 31, 2019
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 24,873	$ 43,015
Gross Unrealized Gains	36	35
Gross Unrealized Losses	(4)
Fair Value	24,905	43,050
Corporate Bonds (Due within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	8,590	14,628
Gross Unrealized Gains	3	20
Gross Unrealized Losses	(4)
Fair Value	8,589	14,648
Commercial Paper (Due within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	5,687	13,406
Fair Value	5,687	13,406
U.S. Government Securities (Due within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	10,596	14,981
Gross Unrealized Gains	33	15
Fair Value	$ 10,629	$ 14,996

Fair Value Measurements and Marketable Securities - Additional Information (Detail)	Mar. 31, 2020 USD ($)
Fair Value Disclosures [Abstract]
Allowance for credit losses	$ 0

Accrued Expenses - Schedule of Accrued Expenses (Detail) - USD ($) $ in Thousands	Mar. 31, 2020	Dec. 31, 2019
Payables And Accruals [Abstract]
Accrued payroll and related expenses	$ 193	$ 37
Accrued professional fees	452	864
Accrued other	236	289
Total accrued expenses	$ 881	$ 1,190

Notes Payable - Additional Information (Detail) - USD ($)		3 Months Ended
	Dec. 29, 2017	Mar. 31, 2020	Mar. 31, 2019	Dec. 31, 2019
Debt Instrument [Line Items]
Proceeds from issuance of notes payable	$ 20,000,000
Unrestricted cash, cash equivalents and marketable debt securities		$ 63,900,000
Credit facility default amount		300,000
Term Loan [Member]
Debt Instrument [Line Items]
Maximum borrowings under term loan	$ 20,000,000	$ 12,700,000
Debt facility description		Upon entering into the Term Loan, the Company became 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 interest at an annual rate of 1.25% above the prime rate, which at March 31, 2020 was 3.25%. 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 interest at annual rate above prime rate	1.25%
Debt facility fee percentage	8.00%
Charges to interest expense of debt outstanding	$ 1,600,000
Loan agreement minimum liquidity required		$ 13,400,000		$ 15,300,000
Debt facility covenant description		Further, since 45 days after the Term Loan was entered in, the Company has met its obligation to maintain a balance of unrestricted cash, cash equivalents and marketable debt 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 Debt 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%
Credit facility default amount		$ 300,000
Interest expense on term loan		$ 300,000	$ 500,000
Debt facility effective interest rate		7.70%
Term Loan [Member] \| Minimum [Member]
Debt Instrument [Line Items]
Percentage equivalent of cash, cash equivalents and marketable debt securities balance		105.00%
Unrestricted cash, cash equivalents and marketable debt securities		$ 55,000,000
Percentage of cash, cash equivalents and marketable debt securities		65.00%
Term Loan [Member] \| Maximum [Member]
Debt Instrument [Line Items]
Aggregate value of cash maintained by Australian subsidiary, limit		$ 4,000,000
Term Loan [Member] \| Prime Rate [Member]
Debt Instrument [Line Items]
Debt facility effective interest rate		3.25%

Notes Payable - Schedule of Notes Payable (Detail) - USD ($) $ in Thousands	Mar. 31, 2020	Dec. 31, 2019
Debt Instruments [Abstract]
Notes payable	$ 12,728	$ 14,545
Less: current portion	(7,273)	(7,273)
Notes payable, net of current portion	5,455	7,272
Accretion related to final payment	1,292	1,192
Notes payable, long term	$ 6,747	$ 8,464

Stock-Based Awards - Additional Information (Detail) - shares	Jan. 01, 2020	Mar. 31, 2020
2014 Stock Option and Incentive Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares available for grant		6,795,572
Shares added to plan	1,497,859
2014 Employee Stock Purchase Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares available for grant		58,611

Stock-Based Awards - Summary of Stock-Based Compensation Expense Related to Stock Options and Restricted Common Stock (Detail) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	$ 710	$ 2,076
Research and Development [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	(144)	960
General and Administrative [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	$ 854	$ 1,116

Commitments and Contingencies - Additional Information (Detail)			3 Months Ended
	Feb. 12, 2019 USD ($) ft²	Oct. 01, 2015	Mar. 31, 2020 USD ($)	Mar. 31, 2019 USD ($)
Other Commitments [Line Items]
Total lease payments over the initial term			$ 10,837,000
Lease expense			303,000	$ 140,000
Operating cash flows from operating leases			300,000	100,000
Additional right-of-use-assets			0	0
Research and Development [Member]
Other Commitments [Line Items]
Lease expense			0	100,000
General and Administrative [Member]
Other Commitments [Line Items]
Lease expense			$ 300,000
General and Administrative [Member] \| Maximum [Member]
Other Commitments [Line Items]
Lease expense				$ 100,000
Boston [Member] \| Massachusetts [Member] \| Shigo Center Plaza Owners LLC [Member]
Other Commitments [Line Items]
Area of office space \| ft²	17,705
Operating lease term	124 months
Lease extension period	60 months
Letter of credit	$ 1,300,000
Operating lease, existence of option to extend	true
Lease rent payment start date	Jun. 21, 2019
Total lease payments over the initial term	$ 10,700,000
Sandiego [Member] \| California [Member]
Other Commitments [Line Items]
Lease expiration date		Dec. 31, 2024

Commitments and Contingencies - Schedule of Future Minimum Lease Payments for Operating Leases (Detail) $ in Thousands	Mar. 31, 2020 USD ($)
Leases [Abstract]
2020 (April - December)	$ 824
2021	1,120
2022	1,143
2023	1,165
2024	1,189
Thereafter	5,396
Total lease payments	10,837
Less: imputed interest	(4,081)
Present value of lease liabilities	$ 6,756

Commitments and Contingencies - Schedule of Components of Leases Expense (Detail) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
Leases [Abstract]
Operating lease cost	$ 331	$ 127
Short-term lease cost		41
Sublease income	(28)	(28)
Total lease cost	$ 303	$ 140

Commitments and Contingencies - Schedule of Weighted Average Remaining Lease Term and Weighted Average Discount Rate of Operating Leases (Detail)	Mar. 31, 2020	Dec. 31, 2019
Leases [Abstract]
Weighted average remaining lease term in years	9 years 2 months 26 days	9 years 5 months 26 days
Weighted average discount rate	11.10%	11.10%

Retirement Plan - Additional Information (Detail) - USD ($) $ in Millions	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
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		$ 0.1
Retirement 401K Plan [Member] \| Maximum [Member]
Defined Contribution Plan Disclosure [Line Items]
Contribution expense	$ 0.1

Australia Research and Development Tax Incentive - Additional Information (Detail) - USD ($)	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019	Dec. 31, 2019
Research and Development Tax Incentive [Line Items]
Unrealized foreign currency exchange gains (losses)	$ (29,000)	$ 14,000
Zafgen Australia Pty Limited [Member]
Research and Development Tax Incentive [Line Items]
Research and development expense	0
Unrealized foreign currency exchange gains (losses)	(200,000)
Zafgen Australia Pty Limited [Member] \| Australia [Member]
Research and Development Tax Incentive [Line Items]
Tax incentive receivable	$ 200,000		$ 200,000
Zafgen Australia Pty Limited [Member] \| Maximum [Member]
Research and Development Tax Incentive [Line Items]
Unrealized foreign currency exchange gains (losses)		$ 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%	43.50%
Reduction to research and development expenses		$ 100,000
Percentage of reduction in research and development costs		43.50%

Restructuring - Additional Information (Detail) $ in Thousands	3 Months Ended	9 Months Ended
	Mar. 31, 2020 USD ($)	Mar. 31, 2020 USD ($) Employee	Dec. 31, 2019 USD ($)
Restructuring Cost And Reserve [Line Items]
Number of workforce reduction \| Employee		20
Restructuring charges	$ 10
Restructuring charges paid	1,738
Accrued restructuring costs	981	$ 981	$ 2,709
Maximum [Member] \| Other Employee Related Costs [Member]
Restructuring Cost And Reserve [Line Items]
Restructuring charges	$ 100

Restructuring - Summary of Accrued Restructuring Costs (Detail) $ in Thousands	3 Months Ended
	Mar. 31, 2020 USD ($)
Restructuring Cost And Reserve [Line Items]
Accrued restructuring costs as of December 31, 2019	$ 2,709
Restructuring charges incurred during the period	10
Amounts paid during the period	(1,738)
Accrued restructuring costs as of March 31, 2020	981
One-Time Employee Termination Benefits [Member]
Restructuring Cost And Reserve [Line Items]
Accrued restructuring costs as of December 31, 2019	2,706
Restructuring charges incurred during the period	10
Amounts paid during the period	(1,735)
Accrued restructuring costs as of March 31, 2020	981
Contract Termination Costs [Member]
Restructuring Cost And Reserve [Line Items]
Accrued restructuring costs as of December 31, 2019	3
Amounts paid during the period	$ (3)

Restructuring - Summary of Restructuring Charges by Category (Detail) $ in Thousands	3 Months Ended
	Mar. 31, 2020 USD ($)
Restructuring Cost And Reserve [Line Items]
Restructuring charges	$ 10
Research and Development [Member]
Restructuring Cost And Reserve [Line Items]
Restructuring charges	10
Cash [Member]
Restructuring Cost And Reserve [Line Items]
Restructuring charges	10
Cash [Member] \| Research and Development [Member]
Restructuring Cost And Reserve [Line Items]
Restructuring charges	$ 10