Larimar Therapeutics (LRMR) 10-Q 7 Nov 17 2017 Q3 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	9 Months Ended
	Sep. 30, 2017	Oct. 31, 2017
Document And Entity Information [Abstract]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Sep. 30, 2017
Document Fiscal Year Focus	2,017
Document Fiscal Period Focus	Q3
Trading Symbol	ZFGN
Entity Registrant Name	Zafgen, Inc.
Entity Central Index Key	1,374,690
Current Fiscal Year End Date	--12-31
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		27,489,457

Condensed Consolidated Balance

Condensed Consolidated Balance Sheets (Unaudited) - USD ($) $ in Thousands	Sep. 30, 2017	Dec. 31, 2016
Current assets:
Cash and cash equivalents	$ 19,193	$ 32,352
Marketable securities	73,987	96,842
Tax incentive receivable	469	347
Prepaid expenses and other current assets	2,007	1,358
Total current assets	95,656	130,899
Property and equipment, net	551	661
Other assets	57	61
Total assets	96,264	131,621
Current liabilities:
Accounts payable	2,676	2,572
Accrued expenses	3,090	3,733
Notes payable, current	1,268	3,589
Total current liabilities	7,034	9,894
Total liabilities	7,034	9,894
Commitments and contingencies (Note 7)
Stockholders' equity:
Preferred stock; $0.001 par value per share; 5,000,000 shares authorized as of September 30, 2017 and December 31, 2016; no shares issued and outstanding as of September 30, 2017 and December 31, 2016
Common stock, $0.001 par value per share; 115,000,000 shares authorized as of September 30, 2017 and December 31, 2016; 27,483,925 and 27,332,551 shares issued and outstanding as of September 30, 2017 and December 31, 2016, respectively	27	27
Additional paid-in capital	365,723	359,329
Accumulated deficit	(276,492)	(237,549)
Accumulated other comprehensive loss	(28)	(80)
Total stockholders' equity	89,230	121,727
Total liabilities and stockholders' equity	$ 96,264	$ 131,621

Condensed Consolidated Balance3

Condensed Consolidated Balance Sheets (Unaudited) (Parenthetical) - $ / shares	Sep. 30, 2017	Dec. 31, 2016
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	27,483,925	27,332,551
Common stock, shares outstanding	27,483,925	27,332,551

Condensed Consolidated Statemen

Condensed Consolidated Statements of Operations and Comprehensive Loss (Unaudited) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Income Statement [Abstract]
Revenue	$ 0	$ 0	$ 0	$ 0
Operating expenses:
Research and development	9,723	10,001	29,928	32,661
General and administrative	3,117	4,830	9,713	15,089
Total operating expenses	12,840	14,831	39,641	47,750
Loss from operations	(12,840)	(14,831)	(39,641)	(47,750)
Other income (expense):
Interest income	266	230	740	664
Interest expense	(31)	(132)	(157)	(432)
Foreign currency transaction gains (losses), net	20	58	115	79
Total other income (expense), net	255	156	698	311
Net loss	$ (12,585)	$ (14,675)	$ (38,943)	$ (47,439)
Net loss per share, basic and diluted	$ (0.46)	$ (0.54)	$ (1.42)	$ (1.74)
Weighted average common shares outstanding, basic and diluted	27,483,550	27,322,907	27,414,314	27,286,323
Comprehensive loss:
Net loss	$ (12,585)	$ (14,675)	$ (38,943)	$ (47,439)
Other comprehensive loss:
Unrealized gain (loss) on marketable securities	13	(52)	52	141
Total other comprehensive income (loss)	13	(52)	52	141
Total comprehensive loss	$ (12,572)	$ (14,727)	$ (38,891)	$ (47,298)

Condensed Consolidated Stateme5

Condensed Consolidated Statements of Cash Flows (Unaudited) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016
Cash flows from operating activities:
Net loss	$ (38,943)	$ (47,439)
Adjustments to reconcile net loss to net cash used in operating activities
Stock-based compensation expense	6,199	8,106
Non-cash interest expense	13	33
Depreciation expense	138	151
Loss on disposal of research and development equipment		328
Unrealized foreign currency transaction gains	(31)	(161)
Premium on marketable securities, net	(297)	(299)
Amortization of premium on marketable securities	219	934
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	(649)	256
Tax incentive receivable	(91)	(250)
Accounts payable	104	(3,557)
Accrued expenses	(610)	(1,411)
Net cash used in operating activities	(33,948)	(43,309)
Cash flows from investing activities:
Proceeds from sales and maturities of marketable securities	112,164	141,366
Purchases of marketable securities	(89,179)	(106,172)
Purchases of property and equipment	(28)	(660)
Net cash provided by investing activities	22,957	34,534
Cash flows from financing activities:
Repayments of notes payable	(2,363)	(2,179)
Proceeds from exercise of common stock options and employee stock purchase plan	195	220
Net cash used in financing activities	(2,168)	(1,959)
Net decrease in cash and cash equivalents	(13,159)	(10,734)
Cash and cash equivalents at beginning of period	32,352	35,595
Cash and cash equivalents at end of period	19,193	24,861
Supplemental disclosure of cash flow information:
Cash paid for interest	$ 130	$ 314

Nature of the Business and Basi

Nature of the Business and Basis of Presentation	9 Months Ended
	Sep. 30, 2017
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 dedicated to significantly improving the health and well-being of patients affected by type 2 diabetes, rare diseases and other metabolic diseases. The Company is focused on developing novel therapeutics that treat the underlying biological mechanisms through the methionine aminopeptidase 2 (“MetAP2”) pathway. The Company has pioneered the study of MetAP2 inhibitors in both common and rare forms of obesity. The Company’s lead product candidate is ZGN-1061, ZGN-1061 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 preclinical 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 September 30, 2017, the Company had an accumulated deficit of $276.5 million. From its inception through September 30, 2017, the Company received net proceeds of $333.3 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 The condensed 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. Unaudited Interim Financial Information The condensed consolidated balance sheet as of December 31, 2016 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, or GAAP. The accompanying unaudited condensed consolidated financial statements as of September 30, 2017 and for the three and nine months ended September 30, 2017 and 2016, have been prepared by the Company, pursuant to the rules and regulations of the Securities and Exchange Commission, or 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, 2016, included in the Company’s Annual Report on Form 10-K,

Summary of Significant Accounti

Summary of Significant Accounting Policies	9 Months Ended
	Sep. 30, 2017
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 securities Marketable securities consist of investments with original maturities greater than 90 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 considers its investment portfolio of investments as available-for-sale. Net Income (Loss) Per Share Basic net income (loss) per share is computed by dividing the net income (loss) attributable to common stockholders by the weighted average number of common shares outstanding for the period. Diluted net income (loss) per share attributable to common stockholders is computed by dividing the diluted net income (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 September 30, 2017 and 2016, from the computation of diluted net loss per share for the three months ended September 30, 2017 and 2016 because they had an anti-dilutive impact due to the net loss incurred for the periods: As of September 30, 2017 2016 Options to purchase common stock 3,963,480 3,220,415 Unvested restricted common stock 5,533 6,637 3,969,013 3,227,052 Recently Issued and Adopted Accounting Pronouncements In May 2014, the Financial Accounting Standards Board (the “FASB”) issued ASU No. 2014-09, Revenue from Contracts with Customers ASU 2016-08 , Revenue from Contract with Customers: Principal versus Agent Considerations ASU 2016-10, Revenue from Contracts with Customers: Identifying Performance Obligations and Licensing ASU 2016-12, Revenue from Contracts with Customers: Narrow-Scope Improvements and Practical Expedients. non-cash In February 2016, the FASB issued ASU No. 2016-02, Leases In March 2016, the FASB issued ASU No. 2016-09, Improvements to Employee Share-Based Payment Accounting paid-in In August 2016, the FASB issued ASU No. 2016-15, Statement of Cash Flows: Classification of Certain Cash Receipts and Cash Payments In May 2017, the FASB issued ASU No. 2017-09, Compensation – Stock Compensation: Scope of Modification Accounting

Fair Value Measurements and Mar

Fair Value Measurements and Marketable Securities	9 Months Ended
	Sep. 30, 2017
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 September 30, 2017 and December 31, 2016, 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 nine months ended September 30, 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 September 30, 2017 and December 31, 2016: September 30, 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 $ 13,823 $ 13,823 $ — $ — Commercial paper 3,499 — 3,499 — Total cash equivalents 17,322 13,823 3,499 — Marketable securities: Corporate bonds 58,747 — 58,747 — Commercial paper 14,760 — 14,760 — Certificates of deposit 480 — 480 — Total marketable securities 73,987 — 73,987 — Total cash equivalents and marketable securities $ 91,309 $ 13,823 $ 77,486 $ — December 31, 2016 Total Quoted Significant Significant (in thousands) Cash equivalents: Money market funds $ 22,091 $ 22,091 $ — $ — Commercial paper 2,997 — 2,997 — Corporate bonds 1,500 — 1,500 — Total cash equivalents 26,588 22,091 4,497 — Marketable securities: Corporate bonds 69,622 — 69,622 — Commercial paper 27,220 — 27,220 — Total marketable securities 96,842 — 96,842 — Total cash equivalents and marketable securities $ 123,430 $ 22,091 $ 101,339 $ — 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 Securities The following tables summarize the Company’s marketable securities as of September 30, 2017 and December 31, 2016: September 30, 2017 Gross Gross Fair Amortized Unrealized Unrealized Cost Gains Losses (in thousands) Assets: Corporate bonds (due within 1 year) $ 58,772 $ — $ (25 ) $ 58,747 Commercial paper (due within 1 year) 14,763 (3 ) 14,760 Certificates of deposit (due within 1 year) 480 — — 480 $ 74,015 $ — $ (28 ) $ 73,987 December 31, 2016 Gross Gross Fair Amortized Unrealized Unrealized Cost Gains Losses (in thousands) Assets: Corporate bonds (due within 1 year) $ 68,777 $ — $ (54 ) $ 68,723 Corporate bonds (due after 1 year through 2 years) 901 — (2 ) 899 Commercial paper (due within 1 year) 27,244 — (24 ) 27,220 $ 96,922 $ — $ (80 ) $ 96,842

Accrued Expenses

Accrued Expenses	9 Months Ended
	Sep. 30, 2017
Payables and Accruals [Abstract]
Accrued Expenses	4. Accrued Expenses Accrued expenses consisted of the following as of September 30, 2017 and December 31, 2016: September 30, December 31, 2017 2016 (in thousands) Accrued payroll and related expenses $ 1,525 $ 2,008 Accrued research and development expenses 1,223 892 Accrued professional fees 267 347 Accrued restructuring — 376 Accrued other 75 110 $ 3,090 $ 3,733

Notes Payable

Notes Payable	9 Months Ended
	Sep. 30, 2017
Debt Disclosure [Abstract]
Notes Payable	5. Notes Payable The Company has outstanding amounts due under a loan and security agreement with Oxford Finance LLC and Midcap Financial, or the 2014 Credit Facility, entered into in March 2014. All promissory notes issued under the 2014 Credit Facility are collateralized by substantially all of the Company’s personal property, other than its intellectual property. There are no financial covenants associated with the 2014 Credit Facility; however, 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; and certain other business transactions. During the three months ended September 30, 2017 and 2016, the Company recognized less than $0.1 million and $0.1 million, respectively, of interest expense related to the 2014 Credit Facility. During the nine months ended September 30, 2017 and 2016, the Company recognized $0.2 million and $0.4 million, respectively, of interest expense related to the 2014 Credit Facility. The effective annual interest rate of the outstanding debt under the 2014 Credit Facility is approximately 10.8%.

Stock-Based Awards

Stock-Based Awards	9 Months Ended
	Sep. 30, 2017
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Stock-Based Awards	6. Stock-Based Awards The Company grants equity awards under its 2014 Stock Option and Incentive Plan, or the 2014 Stock Option Plan, and is authorized to issue common stock under its 2014 Employee Stock Purchase Plan. The Company also has outstanding stock-based awards under its Amended and Restated 2006 Stock Option Plan but is no longer granting awards under this plan. As of September 30, 2017, 2,236,781 shares are available for grant under the 2014 Stock Option Plan, including 1,093,302 shares automatically added to the 2014 Stock Option Plan on January 1, 2017 as a result of a provision in the 2014 Stock Option Plan. The Company recorded stock-based compensation expense related to stock options and restricted common stock in the following expense categories within its condensed consolidated statements of operations: Three Months Nine Months Ended 2017 2016 2017 2016 (in thousands) (in thousands) Research and development $ 896 $ 878 $ 2,629 $ 2,708 General and administrative $ 1,200 1,438 3,570 5,218 $ 2,096 $ 2,316 $ 6,199 $ 7,926

Commitments and Contingencies

Commitments and Contingencies	9 Months Ended
	Sep. 30, 2017
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	7. Commitments and Contingencies Leases The Company has a lease for office space in Boston, Massachusetts, effective as of July 28, 2014, with an initial term expiring July 31, 2017 and an option to extend the lease for three additional years. In March 2015, the Company entered into an operating lease for additional office space in Boston, Massachusetts, effective as of April 15, 2015, with an initial term expiring on July 31, 2017, and two options to extend this lease for three additional years each. 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. In January 2017, the Company extended the leases for both office spaces in Boston, Massachusetts with new terms expiring on July 31, 2020. The Company also has the option to extend both of these leases in Boston, Massachusetts for an additional three years. With the landlord’s consent, the Company has subleased 2,976 square feet of office space in Boston, Massachusetts to an unrelated third party which began on January 1, 2017 and expires on September 30, 2018. The Company expects to receive approximately $0.2 million in sublease rental income during the sublease period, which is recorded as an offset to rental expense in the condensed consolidated statements of operations. Future minimum lease payments for its operating leases as of September 30, 2017 were as follows: Year Ending December 31, (in thousands) 2017 (October to December) $ 118 2018 479 2019 464 2020 226 $ 1,287 During the three months ended September 30, 2017 and 2016, the Company recognized $0.1 million of rental expense related to office space. During the nine months ended September 30, 2017 and 2016, the Company recognized $0.3 million of rental expense related to office space. Intellectual Property Licenses The Company has acquired exclusive rights to develop patented compounds and related know-how As of September 30, 2017, the Company is obligated to make additional milestone payments of up to $12.3 million upon reaching certain pre-commercialization There were no milestones achieved during the three or nine months ended September 30, 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 September 30, 2017, 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 the 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 condensed consolidated financial statements as of September 30, 2017. 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. On October 21, 2015, a purported stockholder of the Company filed a putative class action lawsuit in the U.S. District Court for the District of Massachusetts, against the Company and Thomas E. Hughes, captioned Aviad Bessler v. Zafgen, Inc. and Thomas E. Hughes, No. 1:15-cv-13618. 10b-5 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 September 30, 2017.

Retirement Plan

Retirement Plan	9 Months Ended
	Sep. 30, 2017
Retirement Benefits [Abstract]
Retirement Plan	8. Retirement Plan The Company has a Savings Incentive Match Plan, or SIMPLE IRA, for employees. Under the terms of the plan, the Company contributes 2% 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 September 30, 2017 and 2016, the Company recognized less than $0.1 million of expense related to its contributions to the plan. During the nine months ended September 30, 2017 and 2016, the Company recognized $0.1 million and $0.2 million, respectively, of expense related to its contributions to the plan.

Australia Research and Developm

Australia Research and Development Tax Incentive	9 Months Ended
	Sep. 30, 2017
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 45% refundable tax incentive for qualified research and development activities through December 31, 2016 and 43.5% beginning January 1, 2017. For the three months ended September 30, 2017 and 2016, $0.2 million and nil, respectively, was recorded as a reduction to research and development expenses in the condensed consolidated statements of operations. For the nine months ended September 30, 2017 and 2016, $0.5 million and $0.3 million, respectively, were recorded as a reduction to research and development expenses in the condensed consolidated statements of operations. The refund is denominated in Australian dollars and, therefore, the related receivable is re-measured

Restructuring

Restructuring	9 Months Ended
	Sep. 30, 2017
Restructuring and Related Activities [Abstract]
Restructuring	10. 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 MetAP2 inhibitor, ZGN-1061. ZGN-1061 Nine Months September 30, Year Ended December 31, (in thousands) Restructuring reserve beginning balance $ 376 $ — Restructuring expenses incurred during the period 24 1,223 Amounts paid during the period (400 ) (847 ) Restructuring reserve ending balance $ — $ 376

Subsequent Events

Subsequent Events	9 Months Ended
	Sep. 30, 2017
Subsequent Events [Abstract]
Subsequent Events	11. Subsequent Events In October 2017, the Company granted its newly appointed Chief Executive Officer two inducement stock option grants, which were not granted under the Company’s 2014 Stock Option and Incentive Plan: (i) an option to purchase 550,000 shares of the Company’s common stock with standard vesting terms, and (ii) an additional option to purchase 1,100,000 shares of the Company’s common stock, with such option shares vesting in accordance with certain stock price appreciation and other financial performance goals. Additionally, in October 2017, the Company granted its President and Chief Scientific Officer an option to purchase 275,000 shares of the Company’s common stock under the Company’s 2014 Stock Option and Incentive Plan. Such option will vest in accordance with certain stock price appreciation performance goals.

Summary of Significant Accoun17

Summary of Significant Accounting Policies (Policies)	9 Months Ended
	Sep. 30, 2017
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 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 securities	Marketable securities Marketable securities consist of investments with original maturities greater than 90 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 considers its investment portfolio of investments as available-for-sale.
Net Income (Loss) Per Share	Net Income (Loss) Per Share Basic net income (loss) per share is computed by dividing the net income (loss) attributable to common stockholders by the weighted average number of common shares outstanding for the period. Diluted net income (loss) per share attributable to common stockholders is computed by dividing the diluted net income (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 September 30, 2017 and 2016, from the computation of diluted net loss per share for the three months ended September 30, 2017 and 2016 because they had an anti-dilutive impact due to the net loss incurred for the periods: As of September 30, 2017 2016 Options to purchase common stock 3,963,480 3,220,415 Unvested restricted common stock 5,533 6,637 3,969,013 3,227,052
Recently Issued and Adopted Accounting Pronouncements	Recently Issued and Adopted Accounting Pronouncements In May 2014, the Financial Accounting Standards Board (the “FASB”) issued ASU No. 2014-09, Revenue from Contracts with Customers ASU 2016-08 , Revenue from Contract with Customers: Principal versus Agent Considerations ASU 2016-10, Revenue from Contracts with Customers: Identifying Performance Obligations and Licensing ASU 2016-12, Revenue from Contracts with Customers: Narrow-Scope Improvements and Practical Expedients. non-cash In February 2016, the FASB issued ASU No. 2016-02, Leases In March 2016, the FASB issued ASU No. 2016-09, Improvements to Employee Share-Based Payment Accounting paid-in In August 2016, the FASB issued ASU No. 2016-15, Statement of Cash Flows: Classification of Certain Cash Receipts and Cash Payments In May 2017, the FASB issued ASU No. 2017-09, Compensation – Stock Compensation: Scope of Modification Accounting

Summary of Significant Accoun18

Summary of Significant Accounting Policies (Tables)	9 Months Ended
	Sep. 30, 2017
Accounting Policies [Abstract]
Summary of Common Stock Equivalents Outstanding	The Company excluded the following common stock equivalents, outstanding as of September 30, 2017 and 2016, from the computation of diluted net loss per share for the three months ended September 30, 2017 and 2016 because they had an anti-dilutive impact due to the net loss incurred for the periods: As of September 30, 2017 2016 Options to purchase common stock 3,963,480 3,220,415 Unvested restricted common stock 5,533 6,637 3,969,013 3,227,052

Fair Value Measurements and M19

Fair Value Measurements and Marketable Securities (Tables)	9 Months Ended
	Sep. 30, 2017
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 September 30, 2017 and December 31, 2016: September 30, 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 $ 13,823 $ 13,823 $ — $ — Commercial paper 3,499 — 3,499 — Total cash equivalents 17,322 13,823 3,499 — Marketable securities: Corporate bonds 58,747 — 58,747 — Commercial paper 14,760 — 14,760 — Certificates of deposit 480 — 480 — Total marketable securities 73,987 — 73,987 — Total cash equivalents and marketable securities $ 91,309 $ 13,823 $ 77,486 $ — December 31, 2016 Total Quoted Significant Significant (in thousands) Cash equivalents: Money market funds $ 22,091 $ 22,091 $ — $ — Commercial paper 2,997 — 2,997 — Corporate bonds 1,500 — 1,500 — Total cash equivalents 26,588 22,091 4,497 — Marketable securities: Corporate bonds 69,622 — 69,622 — Commercial paper 27,220 — 27,220 — Total marketable securities 96,842 — 96,842 — Total cash equivalents and marketable securities $ 123,430 $ 22,091 $ 101,339 $ —
Summary of Marketable Securities	The following tables summarize the Company’s marketable securities as of September 30, 2017 and December 31, 2016: September 30, 2017 Gross Gross Fair Amortized Unrealized Unrealized Cost Gains Losses (in thousands) Assets: Corporate bonds (due within 1 year) $ 58,772 $ — $ (25 ) $ 58,747 Commercial paper (due within 1 year) 14,763 (3 ) 14,760 Certificates of deposit (due within 1 year) 480 — — 480 $ 74,015 $ — $ (28 ) $ 73,987 December 31, 2016 Gross Gross Fair Amortized Unrealized Unrealized Cost Gains Losses (in thousands) Assets: Corporate bonds (due within 1 year) $ 68,777 $ — $ (54 ) $ 68,723 Corporate bonds (due after 1 year through 2 years) 901 — (2 ) 899 Commercial paper (due within 1 year) 27,244 — (24 ) 27,220 $ 96,922 $ — $ (80 ) $ 96,842

Accrued Expenses (Tables)

Accrued Expenses (Tables)	9 Months Ended
	Sep. 30, 2017
Payables and Accruals [Abstract]
Schedule of Accrued Expenses	Accrued expenses consisted of the following as of September 30, 2017 and December 31, 2016: September 30, December 31, 2017 2016 (in thousands) Accrued payroll and related expenses $ 1,525 $ 2,008 Accrued research and development expenses 1,223 892 Accrued professional fees 267 347 Accrued restructuring — 376 Accrued other 75 110 $ 3,090 $ 3,733

Stock-Based Awards (Tables)

Stock-Based Awards (Tables)	9 Months Ended
	Sep. 30, 2017
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
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 condensed consolidated statements of operations: Three Months Nine Months Ended 2017 2016 2017 2016 (in thousands) (in thousands) Research and development $ 896 $ 878 $ 2,629 $ 2,708 General and administrative $ 1,200 1,438 3,570 5,218 $ 2,096 $ 2,316 $ 6,199 $ 7,926

Commitments and Contingencies (

Commitments and Contingencies (Tables)	9 Months Ended
	Sep. 30, 2017
Commitments and Contingencies Disclosure [Abstract]
Schedule of Future Minimum Lease Payments for Operating Leases	Future minimum lease payments for its operating leases as of September 30, 2017 were as follows: Year Ending December 31, (in thousands) 2017 (October to December) $ 118 2018 479 2019 464 2020 226 $ 1,287

Restructuring (Tables)

Restructuring (Tables)	9 Months Ended
	Sep. 30, 2017
Restructuring and Related Activities [Abstract]
Summary of Restructuring Reserve	The following table summarizes the restructuring reserve for the periods indicated: Nine Months September 30, Year Ended December 31, (in thousands) Restructuring reserve beginning balance $ 376 $ — Restructuring expenses incurred during the period 24 1,223 Amounts paid during the period (400 ) (847 ) Restructuring reserve ending balance $ — $ 376

Nature of the Business and Ba24

Nature of the Business and Basis of Presentation - Additional Information (Detail) - USD ($) $ in Thousands	9 Months Ended	142 Months Ended
	Sep. 30, 2017	Sep. 30, 2017	Dec. 31, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Entity incorporation date	Nov. 22, 2005
Accumulated deficit	$ (276,492)	$ (276,492)	$ (237,549)
Net proceeds from sale of securities		333,300
Total cash, cash equivalents and marketable securities	$ 93,180	$ 93,180

Summary of Significant Accoun25

Summary of Significant Accounting Policies - Summary of Common Stock Equivalents Outstanding (Detail) - shares	9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	3,969,013	3,227,052
Options to Purchase Common Stock [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	3,963,480	3,220,415
Unvested Restricted Common Stock [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	5,533	6,637

Fair Value Measurements and M26

Fair Value Measurements and Marketable Securities - Additional Information (Detail)	Sep. 30, 2017USD ($)
Fair Value Disclosures [Abstract]
Transfers of financial assets between level 1 and level 2	$ 0

Fair Value Measurements and M27

Fair Value Measurements and Marketable Securities - Summary of Cash Equivalents and Marketable Securities (Detail) - USD ($) $ in Thousands	Sep. 30, 2017	Dec. 31, 2016
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	$ 17,322	$ 26,588
Marketable securities	73,987	96,842
Total cash equivalents and marketable securities	91,309	123,430
Money Market Funds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	13,823	22,091
Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	3,499	2,997
Marketable securities	14,760	27,220
Corporate Bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents		1,500
Marketable securities	58,747	69,622
Certificates of Deposit [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Marketable securities	480
Quoted Prices in Active Markets, (Level 1) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	13,823	22,091
Total cash equivalents and marketable securities	13,823	22,091
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	13,823	22,091
Significant Other Observable Inputs (Level 2) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	3,499	4,497
Marketable securities	73,987	96,842
Total cash equivalents and marketable securities	77,486	101,339
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	3,499	2,997
Marketable securities	14,760	27,220
Significant Other Observable Inputs (Level 2) [Member] | Corporate Bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents		1,500
Marketable securities	58,747	$ 69,622
Significant Other Observable Inputs (Level 2) [Member] | Certificates of Deposit [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Marketable securities	$ 480

Fair Value Measurements and M28

Fair Value Measurements and Marketable Securities - Summary of Marketable Securities (Detail) - USD ($) $ in Thousands	Sep. 30, 2017	Dec. 31, 2016
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 74,015	$ 96,922
Gross Unrealized Gains	0	0
Gross Unrealized Losses	(28)	(80)
Fair Value	73,987	96,842
Corporate Bonds (Due within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	58,772	68,777
Gross Unrealized Gains	0	0
Gross Unrealized Losses	(25)	(54)
Fair Value	58,747	68,723
Commercial Paper (Due within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	14,763	27,244
Gross Unrealized Gains	0	0
Gross Unrealized Losses	(3)	(24)
Fair Value	14,760	27,220
Corporate Bonds (Due After 1 Year Through 2 Years) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost		901
Gross Unrealized Gains		0
Gross Unrealized Losses		(2)
Fair Value		$ 899
Certificates of Deposit (Due within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	480
Gross Unrealized Gains	0
Fair Value	$ 480

Accrued Expenses - Schedule of

Accrued Expenses - Schedule of Accrued Expenses (Detail) - USD ($) $ in Thousands	Sep. 30, 2017	Dec. 31, 2016
Payables and Accruals [Abstract]
Accrued payroll and related expenses	$ 1,525	$ 2,008
Accrued research and development expenses	1,223	892
Accrued professional fees	267	347
Accrued restructuring		376
Accrued other	75	110
Accrued expenses	$ 3,090	$ 3,733

Notes Payable - Additional Info

Notes Payable - Additional Information (Detail) - 2014 Credit Facility [Member] - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Debt Instrument [Line Items]
Covenants under credit facility			There are no financial covenants associated with the 2014 Credit Facility; however, 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; and certain other business transactions.
Secured Debt [Member]
Debt Instrument [Line Items]
Interest expense on credit facility		$ 100,000	$ 200,000	$ 400,000
Effective annual interest rate	10.80%		10.80%
Maximum [Member] | Secured Debt [Member]
Debt Instrument [Line Items]
Interest expense on credit facility	$ 100,000

Stock-Based Awards - Additional

Stock-Based Awards - Additional Information (Detail) - 2014 Stock Option and Incentive Plan [Member] - shares	Jan. 01, 2017	Sep. 30, 2017
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares added to plan	1,093,302
Shares available for grant		2,236,781

Stock-Based Awards - Summary of

Stock-Based Awards - Summary of Stock-Based Compensation Expense Related to Stock Options and Restricted Common Stock (Detail) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	$ 2,096	$ 2,316	$ 6,199	$ 7,926
Research and Development [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	896	878	2,629	2,708
General and Administrative [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	$ 1,200	$ 1,438	$ 3,570	$ 5,218

Commitments and Contingencies -

Commitments and Contingencies - Additional Information (Detail)	Jan. 01, 2017ft²	Oct. 01, 2015	Apr. 15, 2015Option	Jul. 28, 2014	Jan. 31, 2017	Sep. 30, 2017USD ($)	Sep. 30, 2016USD ($)	Sep. 30, 2017USD ($)	Sep. 30, 2016USD ($)	Sep. 30, 2018USD ($)
Other Commitments [Line Items]
Operating lease, rental expense						$ 100,000	$ 100,000	$ 300,000	$ 300,000
Subsequent Licensed Product [Member]
Other Commitments [Line Items]
Licensing fees per product maximum						1,300,000		1,300,000
Development Based Milestones [Member]
Other Commitments [Line Items]
Milestone payments due						0	$ 0	$ 0	$ 0
Boston Office Space [Member]
Other Commitments [Line Items]
Lease expiration date				Jul. 31, 2017	Jul. 31, 2020			Jul. 31, 2020
Lease extension period				3 years				3 years
Boston Office Space [Member] | Unrelated Third Party Member
Other Commitments [Line Items]
Subleased area | ft²	2,976
Sublease expiration date	Sep. 30, 2018
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, 2017					Jul. 31, 2020
Lease extension period			3 years
Number of options to extend lease | Option			2
San Diego Office Space [Member]
Other Commitments [Line Items]
Lease expiration date		Sep. 30, 2019
Lease extension period		5 years
Maximum [Member] | Pre Commercialization Milestones [Member]
Other Commitments [Line Items]
Milestone payments						12,300,000		$ 12,300,000
Maximum [Member] | Product Commercialization Milestones [Member]
Other Commitments [Line Items]
Milestone payments						$ 12,500,000		$ 12,500,000

Commitments and Contingencies34

Commitments and Contingencies - Schedule of Future Minimum Lease Payments for Operating Leases (Detail) $ in Thousands	Sep. 30, 2017USD ($)
Commitments and Contingencies Disclosure [Abstract]
2017 (October to December)	$ 118
2,018	479
2,019	464
2,020	226
Total	$ 1,287

Retirement Plan - Additional In

Retirement Plan - Additional Information (Detail) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016
Defined Contribution Plan Disclosure [Line Items]
Percentage of employer's contribution on employee's base salary			2.00%
Contribution expense			$ 100,000	$ 200,000
Maximum [Member]
Defined Contribution Plan Disclosure [Line Items]
Contribution expense	$ 100,000	$ 100,000

Australia Research and Develo36

Australia Research and Development Tax Incentive - Additional Information (Detail) - USD ($)	3 Months Ended		9 Months Ended		12 Months Ended
	Sep. 30, 2017	Sep. 30, 2016	Sep. 30, 2017	Sep. 30, 2016	Dec. 31, 2016
Research and Development Tax Incentive [Line Items]
Unrealized foreign currency transaction gains (losses)			$ 31,000	$ 161,000
Zafgen Australia Pty Limited [Member]
Research and Development Tax Incentive [Line Items]
Unrealized foreign currency transaction gains (losses)				100,000
Zafgen Australia Pty Limited [Member] | Australia [Member]
Research and Development Tax Incentive [Line Items]
Tax incentive receivable	$ 500,000		$ 500,000		$ 300,000
Zafgen Australia Pty Limited [Member] | Research and Development [Member]
Research and Development Tax Incentive [Line Items]
Percentage of refundable tax incentive			43.50%		45.00%
Reduction to research and development expenses	200,000	$ 0	$ 500,000	$ 300,000
Zafgen Australia Pty Limited [Member] | Maximum [Member]
Research and Development Tax Incentive [Line Items]
Unrealized foreign currency transaction gains (losses)	$ 100,000	$ 100,000	$ 100,000

Restructuring - Additional Info

Restructuring - Additional Information (Detail)	1 Months Ended
	Dec. 31, 2016
Restructuring and Related Activities [Abstract]
Percentage of workforce reduction	31.00%

Restructuring - Summary of Rest

Restructuring - Summary of Restructuring Reserve (Detail) - USD ($) $ in Thousands	9 Months Ended	12 Months Ended
	Sep. 30, 2017	Dec. 31, 2016
Restructuring Reserve [Abstract]
Restructuring reserve beginning balance	$ 376
Restructuring expenses incurred during the period	24	$ 1,223
Amounts paid during the period	$ (400)	(847)
Restructuring reserve ending balance		$ 376

Subsequent Events - Additional

Subsequent Events - Additional Information (Detail) - Subsequent Event [Member]	1 Months Ended
	Oct. 31, 2017shares
Chief Executive Officer [Member]
Subsequent Event [Line Items]
Stock option granted	550,000
Chief Executive Officer [Member] | Stock Appreciation Rights (SARs) [Member]
Subsequent Event [Line Items]
Additional stock option to purchase common stock	1,100,000
2014 Stock Option and Incentive Plan [Member] | President and Chief Scientific Officer [Member]
Subsequent Event [Line Items]
Stock option granted	275,000