Larimar Therapeutics (LRMR) 10-K 10 Mar 17 2016 FY Annual report Financial data

Document and Entity Information

Document and Entity Information - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2016	Mar. 01, 2017	Jun. 30, 2016
Document And Entity Information [Abstract]
Document Type	10-K
Amendment Flag	false
Document Period End Date	Dec. 31, 2016
Document Fiscal Year Focus	2,016
Document Fiscal Period Focus	FY
Trading Symbol	ZFGN
Entity Registrant Name	Zafgen, Inc.
Entity Central Index Key	1,374,690
Current Fiscal Year End Date	--12-31
Entity Well-known Seasoned Issuer	No
Entity Current Reporting Status	Yes
Entity Voluntary Filers	No
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		27,350,723
Entity Public Float			$ 65.7

Consolidated Balance Sheets

Consolidated Balance Sheets - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 32,352	$ 35,595
Marketable securities	96,842	149,484
Tax incentive receivable	347	1,323
Prepaid expenses and other current assets	1,358	1,708
Total current assets	130,899	188,110
Property and equipment, net	661	902
Other assets	61	94
Total assets	131,621	189,106
Current liabilities:
Accounts payable	2,572	7,495
Accrued expenses	3,733	6,112
Notes payable, current	3,589	2,936
Total current liabilities	9,894	16,543
Notes payable, net of discount, long-term		3,453
Total liabilities	9,894	19,996
Commitments and contingencies (Note 10)
Stockholders' equity:
Preferred stock; $0.001 par value per share; 5,000,000 shares authorized as of December 31, 2016 and 2015; no shares issued and outstanding as of December 31, 2016 and 2015
Common stock, $0.001 par value per share; 115,000,000 shares authorized as of December 31, 2016 and 2015; 27,332,551 and 27,242,503 shares issued and outstanding as of December 31, 2016 and 2015, respectively	27	27
Additional paid-in capital	359,329	348,961
Accumulated deficit	(237,549)	(179,671)
Accumulated other comprehensive loss	(80)	(207)
Total stockholders' equity	121,727	169,110
Total liabilities and stockholders' equity	$ 131,621	$ 189,106

Consolidated Balance Sheets (Pa

Consolidated Balance Sheets (Parenthetical) - $ / shares	Dec. 31, 2016	Dec. 31, 2015
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	27,332,551	27,242,503
Common stock, shares outstanding	27,332,551	27,242,503

Consolidated Statements of Oper

Consolidated Statements of Operations and Comprehensive Loss - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Income Statement [Abstract]
Revenue	$ 0	$ 0	$ 0
Operating expenses:
Research and development	39,936	54,618	27,391
General and administrative	18,289	19,195	8,141
Total operating expenses	58,225	73,813	35,532
Loss from operations	(58,225)	(73,813)	(35,532)
Other income (expense):
Interest income	894	438	28
Interest expense	(529)	(806)	(870)
Foreign currency transaction gains (losses), net	(18)	(105)	(104)
Total other income (expense), net	347	(473)	(946)
Net loss	(57,878)	(74,286)	(36,478)
Accretion of redeemable convertible preferred stock to redemption value			(92)
Net loss attributable to common stockholders	$ (57,878)	$ (74,286)	$ (36,570)
Net loss per share attributable to common stockholders, basic and diluted	$ (2.12)	$ (2.78)	$ (3)
Weighted average common shares outstanding, basic and diluted	27,297,934	26,756,079	12,189,155
Comprehensive loss:
Net loss	$ (57,878)	$ (74,286)	$ (36,478)
Other comprehensive loss:
Unrealized gain (loss) on marketable securities	127	(172)	(35)
Total other comprehensive loss	127	(172)	(35)
Total comprehensive loss	$ (57,751)	$ (74,458)	$ (36,513)

Consolidated Statements of Chan

Consolidated Statements of Changes in Redeemable Convertible Preferred Stock and Stockholders' Equity (Deficit) - USD ($) $ in Thousands	Total	Redeemable Convertible Preferred Stock [Member]	Redeemable Convertible Preferred Stock [Member]Series E Preferred Stock [Member]	Common Stock [Member]	Additional Paid-in Capital [Member]	Accumulated Deficit [Member]	Accumulated Other Comprehensive Loss [Member]
Beginning balance at Dec. 31, 2013	$ (68,574)			$ 1	$ 332	$ (68,907)
Issuance of redeemable convertible preferred stock, value			$ 442
Beginning balance, shares at Dec. 31, 2013				729,391
Temporary equity, beginning balance at Dec. 31, 2013		$ 103,797
Temporary equity, beginning balance, shares at Dec. 31, 2013		94,483,404
Accretion of redeemable convertible preferred stock to redemption value	(92)	$ 92			(92)
Conversion of redeemable convertible preferred stock to common stock, value	104,331	$ (104,331)		$ 15	104,316
Conversion of redeemable convertible preferred stock to common stock, shares		(94,687,505)		15,077,621
Issuance of common stock	100,164			$ 7	100,157
Issuance of common stock, shares			204,101	6,900,000
Issuance of common stock upon exercise of stock options, value	3				3
Issuance of common stock upon exercise of stock options, shares				398
Issuance of common stock in lieu of milestone payment	3,569				3,569
Issuance of common stock in lieu of milestone payment, shares				171,750
Stock-based compensation expense	1,553				1,553
Unrealized gain (loss) on marketable securities	(35)						$ (35)
Net loss	(36,478)					(36,478)
Ending balance at Dec. 31, 2014	104,441			$ 23	209,838	(105,385)	(35)
Ending balance, shares at Dec. 31, 2014				22,879,160
Issuance of common stock upon exercise of stock options and employee stock purchase plan	974				974
Issuance of common stock upon exercise of stock options and employee stock purchase plan, shares				418,241
Issuance of common stock	129,571			$ 4	129,567
Issuance of common stock, shares				3,942,200
Issuance of restricted stock units	0	$ 0		$ 0	0	0	0
Issuance of restricted stock units, shares				2,902
Stock-based compensation expense	8,582				8,582
Unrealized gain (loss) on marketable securities	(172)						(172)
Net loss	(74,286)					(74,286)
Ending balance at Dec. 31, 2015	169,110			$ 27	348,961	(179,671)	(207)
Ending balance, shares at Dec. 31, 2015				27,242,503
Issuance of common stock upon exercise of stock options and employee stock purchase plan	220				220
Issuance of common stock upon exercise of stock options and employee stock purchase plan, shares				72,663
Issuance of common stock	35				35
Issuance of common stock, shares				5,564
Issuance of restricted stock units	$ 0	$ 0		$ 0	0	0	0
Issuance of common stock upon exercise of stock options, shares	35,000
Issuance of restricted stock units, shares				11,821
Stock-based compensation expense	$ 10,113				10,113
Unrealized gain (loss) on marketable securities	127						127
Net loss	(57,878)					(57,878)
Ending balance at Dec. 31, 2016	$ 121,727			$ 27	$ 359,329	$ (237,549)	$ (80)
Ending balance, shares at Dec. 31, 2016				27,332,551

Consolidated Statements of Cha6

Consolidated Statements of Changes in Redeemable Convertible Preferred Stock and Stockholders' Equity (Deficit) (Parenthetical) $ in Thousands	12 Months Ended
	Dec. 31, 2014USD ($)
Issuance of redeemable convertible preferred stock, issuance costs	$ 2,312
Series E Preferred Stock [Member]
Issuance of redeemable convertible preferred stock, issuance costs	$ 1

Consolidated Statements of Cash

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Cash flows from operating activities:
Net loss	$ (57,878)	$ (74,286)	$ (36,478)
Adjustments to reconcile net loss to net cash used in operating activities
Stock-based compensation expense	10,113	8,582	1,553
Non-cash interest expense	43	62	46
Depreciation expense	212	70	16
Loss on disposal of research and development equipment	328
Common stock issued in lieu of milestone payment			3,569
Unrealized foreign currency transaction losses	6	82	93
Premium on marketable securities, net	(340)	(2,036)	(225)
Amortization of premium on marketable securities	1,037	1,243	31
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	413	(363)	(1,121)
Tax incentive receivable	970	(1,014)	1,133
Accounts payable	(4,625)	4,914	815
Accrued expenses	(2,254)	3,192	2,327
Net cash used in operating activities	(51,975)	(59,554)	(28,241)
Cash flows from investing activities:
Proceeds from sales and maturities of marketable securities	188,600	195,987
Purchases of marketable securities	(136,528)	(287,491)	(57,200)
Purchases of property and equipment	(660)	(595)	(58)
Deposits for leased property	35	(19)	(57)
Net cash provided by (used in) investing activities	51,447	(92,118)	(57,315)
Cash flows from financing activities:
Proceeds from issuance of redeemable convertible preferred stock, net of issuance costs			442
Proceeds from issuance of notes payable, net of issuance costs			7,386
Payments of debt offering costs			(49)
Repayments of notes payable	(2,935)	(1,381)
Proceeds from exercise of common stock options and employee stock purchase plan	220	974	3
Proceeds from public offerings, net of commissions and underwriting discounts		130,044	102,672
Payments of public offering costs		(473)	(2,312)
Net cash (used in) provided by financing activities	(2,715)	129,164	108,142
Net (decrease) increase in cash and cash equivalents	(3,243)	(22,508)	22,586
Cash and cash equivalents at beginning of period	35,595	58,103	35,517
Cash and cash equivalents at end of period	32,352	35,595	58,103
Supplemental disclosure of non-cash investing and financing activities:
Accretion of redeemable convertible preferred stock to redemption values			92
Deferred offering costs included in accounts payable and accrued expenses			148
Property and equipment included in accounts payable		298
Conversion of redeemable preferred stock to common stock			104,331
Conversion of milestone liabilities to common stock			3,569
Supplemental disclosure of cash flow information:
Cash paid for interest	$ 388	$ 584	$ 632

Nature of the Business and Basi

Nature of the Business and Basis of Presentation	12 Months Ended
	Dec. 31, 2016
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 metabolic diseases including type 2 diabetes and obesity. 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, On July 19, 2016, the Company announced that it was refocusing its resources on the development of ZGN-1061 pre-clinical 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 pre-clinical The Company’s product candidates are all in the development stage. There can be no assurance that the Company’s research and development will be successfully completed, that adequate protection for the Company’s intellectual property will be obtained, that any product candidates developed will obtain necessary government regulatory approval or that any approved products will be commercially viable. Even if the Company’s product development efforts are successful, it is uncertain when, if ever, the Company will generate significant revenue from product sales. The Company operates in an environment of rapid change in technology and substantial competition from pharmaceutical and biotechnology companies. In addition, the Company is dependent upon the services of its employees and consultants. The Company has incurred losses and negative cash flows from operations since its inception. As of December 31, 2016, the Company had an accumulated deficit of $237.5 million. From its inception through December 31, 2016, 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 consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries Zafgen Securities Corporation, Zafgen Australia Pty Limited, and Zafgen Animal Health, LLC. All intercompany balances and transactions have been eliminated. The accompanying consolidated financial statements have been prepared in conformity with accounting principles generally accepted in the United States of America (“GAAP”).

Summary of Significant Accounti

Summary of Significant Accounting Policies	12 Months Ended
	Dec. 31, 2016
Accounting Policies [Abstract]
Summary of Significant Accounting Policies	2. Summary of Significant Accounting Policies Use of Estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities as of the date of the consolidated financial statements, and the reported amounts of expenses during the reporting periods. Significant estimates and assumptions reflected in these consolidated financial statements include, but are not limited to, the accrual of research and development expenses and the valuation of stock-based awards. Estimates are periodically reviewed in light of changes in circumstances, facts and experience. Actual results could differ from the Company’s estimates. Cash Equivalents The Company considers all short-term, highly liquid investments with original maturities of ninety days or less at acquisition date to be cash equivalents. Cash equivalents, which consist of money market funds, U.S. government securities, corporate bonds, and commercial paper, are stated at fair value. Concentration of Credit Risk and of Significant Suppliers Financial instruments that potentially expose the Company to concentrations of credit risk consist primarily of cash, cash equivalents and marketable securities. The Company has all cash, cash equivalents and marketable securities balances at two accredited financial institutions in amounts that exceed federally insured limits. The Company does not believe that it is subject to unusual credit risk beyond the normal credit risk associated with commercial banking relationships. The Company is dependent on third-party manufacturers to supply products for research and development activities in its programs. In particular, the Company relies and expects to continue to rely on a small number of manufacturers to supply it with its requirements for the active pharmaceutical ingredients and formulated drugs related to these programs. These programs could be adversely affected by a significant interruption in the supply of active pharmaceutical ingredients and formulated drugs. Marketable securities Marketable securities consist of investments with original maturities greater than ninety days. The Company has classified its investments with maturities beyond one year as short term, based on their highly liquid nature and because such marketable securities represent the investment of cash that is available for current operations. The Company considers its investment portfolio of investments as available-for-sale. Deferred Offering Costs The Company capitalizes certain legal, accounting and other third-party fees that are directly associated with in-process paid-in Property and Equipment Property and equipment are stated at cost less accumulated depreciation. Depreciation expense is recognized using the straight-line method over a five-year estimated useful life for equipment, furniture and fixtures and office equipment. Leasehold improvements are amortized over the shorter of the asset life or the term of the lease agreement. Expenditures for repairs and maintenance of assets are charged to expense as incurred. Upon retirement or sale, the cost and related accumulated depreciation of assets disposed of are removed from the accounts and any resulting gain or loss is included in loss from operations. Impairment of Long-Lived Assets Long-lived assets consist of property and equipment. Long-lived assets to be held and used are tested for recoverability whenever events or changes in business circumstances indicate that the carrying amount of the assets may not be fully recoverable. Factors that the Company considers in deciding when to perform an impairment review include significant underperformance of the business in relation to expectations, significant negative industry or economic trends, and significant changes or planned changes in the use of the assets. If an impairment review is performed to evaluate a long-lived asset for recoverability, the Company compares forecasts of undiscounted cash flows expected to result from the use and eventual disposition of the long-lived asset to its carrying value. An impairment loss would be recognized when estimated undiscounted future cash flows expected to result from the use of an asset are less than its carrying amount. The impairment loss would be based on the excess of the carrying value of the impaired asset over its fair value, determined based on discounted cash flows. To date, the Company has not recorded any impairment losses on long-lived assets. Research and Development Costs Research and development costs are expensed as incurred. Included in research and development expenses are wages, stock-based compensation and benefits of employees, third-party license fees and milestones and other operational costs related to the Company’s research and development activities, including facility-related expenses and external costs of outside vendors engaged to conduct pre-clinical Research Contract Costs and Accruals The Company has entered into various research and development contracts with research institutions and other companies both inside and outside of the United States. These agreements are generally cancelable, and related payments are recorded as research and development expenses as incurred. The Company records accruals for estimated ongoing research costs. When evaluating the adequacy of the accrued liabilities, the Company analyzes progress of the studies, including the phase or completion of events, invoices received and contracted costs. Significant judgments and estimates are made in determining the accrued balances at the end of any reporting period. Actual results could differ from the Company’s estimates. The Company’s historical accrual estimates have not been materially different from the actual costs. Patent Costs All patent-related costs incurred in connection with filing and prosecuting patent applications are recorded as general and administrative expenses as incurred, as recoverability of such expenditures is uncertain. Accounting for Stock-Based Compensation The Company measures all stock options and other stock-based awards granted to employees and directors at the fair value on the date of the grant using the Black-Scholes option-pricing model. The fair value of the awards is recognized as expense, net of estimated forfeitures, over the requisite service period, which is generally the vesting period of the respective award. The straight-line method of expense recognition is applied to all awards with service-only conditions. For stock-based awards granted to consultants and nonemployees, compensation expense is recognized over the period during which services are rendered by such consultants and nonemployees until completed. At the end of each financial reporting period prior to completion of the service, the fair value of these awards is re-measured The Company classifies stock-based compensation expense in its consolidated statement of operations and comprehensive loss in the same manner in which the award recipient’s payroll costs are classified or in which the award recipients’ service payments are classified. The Company recognizes compensation expense for only the portion of awards that are expected to vest. In developing a forfeiture rate estimate, the Company has considered its historical experience to estimate pre-vesting Income Taxes The Company accounts for income taxes using the asset and liability method, which requires the recognition of deferred tax assets and liabilities for the expected future tax consequences of events that have been recognized in the consolidated financial statements or in the Company’s tax returns. Deferred taxes are determined based on the difference between the financial statement and tax basis of assets and liabilities using enacted tax rates in effect in the years in which the differences are expected to reverse. Changes in deferred tax assets and liabilities are recorded in the provision for income taxes. The Company assesses the likelihood that its deferred tax assets will be recovered from future taxable income and, to the extent it believes, based upon the weight of available evidence, that it is more likely than not that all or a portion of deferred tax assets will not be realized, a valuation allowance is established through a charge to income tax expense. Potential for recovery of deferred tax assets is evaluated by estimating the future taxable profits expected and considering prudent and feasible tax planning strategies. The Company accounts for uncertainty in income taxes recognized in the consolidated financial statements by applying a two-step more-likely-than-not Segment Data The Company manages its operations as a single segment for the purposes of assessing performance and making operating decisions. The Company’s singular focus is on advancing novel therapeutics for patients suffering from type 2 diabetes, severe obesity and obesity-related disorders. No revenue has been generated since inception, and all tangible assets are held in the United States. Comprehensive Loss Comprehensive loss includes net loss as well as other changes in stockholders’ equity (deficit) that result from transactions and economic events other than those with stockholders. For the years ended December 31, 2016, 2015 and 2014, the Company’s only element of other comprehensive loss was unrealized gain or loss on marketable securities. Net Income (Loss) Per Share Upon the closing of the Company’s IPO in June 2014, all of the Company’s outstanding redeemable convertible preferred shares were converted into shares of common stock. Prior to this conversion, the Company followed the two-class two-class two-class two-class 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. 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 2016-08 , Revenue from Contract with Customers: Principal versus Agent Considerations 2016-10, Revenue from Contracts with Customers: Identifying Performance Obligations and Licensing 2016-12, Revenue from Contracts with Customers: Narrow-Scope Improvements and Practical Expedients. non-cash In August 2014, the FASB issued ASU No. 2014-15, Presentation of Financial Statements—Going Concern In November 2015, the FASB issued ASU No. 2015-17, Balance Sheet Classification of Deferred Taxes. 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 In August 2016, the FASB issued ASU No. 2016-15, Statement of Cash Flows: Classification of Certain Cash Receipts and Cash Payments Reclassifications Prior period financial statement amounts have been reclassified to conform to current period presentation.

Fair Value Measurements and Mar

Fair Value Measurements and Marketable Securities	12 Months Ended
	Dec. 31, 2016
Fair Value Disclosures [Abstract]
Fair Value Measurements and Marketable Securities	3. Fair Value Measurements and Marketable Securities Fair Value Measurements The following tables present information about the Company’s financial assets that have been measured at fair value as of December 31, 2016 and 2015, 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 securities as of December 31, 2016 and 2015: 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 $ — December 31, 2015 Total Quoted Significant Significant (in thousands) Cash equivalents: Money market funds $ 13,231 $ 13,231 $ — $ — U.S. government securities 4,999 — 4,999 — Commercial paper 4,697 — 4,697 — Corporate bonds 3,000 — 3,000 — Total cash equivalents 25,927 13,231 12,696 — Marketable securities: Corporate bonds 125,516 — 125,516 — Commercial paper 19,468 — 19,468 — U.S. government securities 4,500 — 4,500 — Total marketable securities 149,484 — 149,484 — Total cash equivalents and marketable securities $ 175,411 $ 13,231 $ 162,180 $ — The carrying amounts reflected in the consolidated balance sheets for tax incentive receivable, accounts payable, and accrued expenses approximate fair value due to their short-term maturities. The carrying value of the Company’s outstanding notes payable approximates fair value (a Level 2 fair value measurement), reflecting interest rates currently available to the Company. Marketable Securities The following tables summarize the Company’s marketable securities as of December 31, 2016 and 2015: December 31, 2016 Amortized Gross Gross Fair Value (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 December 31, 2015 Amortized Gross Gross Fair Value (in thousands) Assets: Corporate bonds (due within 1 year) $ 112,828 $ 1 $ (169 ) $ 112,660 Corporate bonds (due after 1 year through 2 years) 12,885 3 (32 ) 12,856 Commercial paper (due within 1 year) 19,478 — (10 ) 19,468 U.S. government securities (due within 1 year) 4,500 — — 4,500 $ 149,691 $ 4 $ (211 ) $ 149,484

Property and Equipment, net

Property and Equipment, net	12 Months Ended
	Dec. 31, 2016
Property, Plant and Equipment [Abstract]
Property and Equipment, net	4. Property and Equipment, net Property and equipment, net consisted of the following as of December 31, 2016 and 2015: December 31, Useful Life 2016 2015 (in thousands) Office equipment 5 years $ 372 $ 359 Furniture and fixtures 5 years 194 186 Equipment 5 years — 71 Leasehold improvements * 415 406 981 1,022 Less: Accumulated depreciation (320 ) (120 ) $ 661 $ 902 * shorter of asset life or lease term Depreciation expense was $0.2 million, $0.1 million and less than $0.1 million for the years ended December 31, 2016, 2015 and 2014, respectively.

Accrued Expenses

Accrued Expenses	12 Months Ended
	Dec. 31, 2016
Payables and Accruals [Abstract]
Accrued Expenses	5. Accrued Expenses Accrued expenses consisted of the following as of December 31, 2016 and 2015: December 31, 2016 2015 (in thousands) Accrued payroll and related expenses $ 2,008 $ 1,802 Accrued research and development expenses 892 3,727 Accrued restructuring 376 — Accrued professional fees 347 422 Accrued other 110 161 $ 3,733 $ 6,112

Notes Payable

Notes Payable	12 Months Ended
	Dec. 31, 2016
Debt Disclosure [Abstract]
Notes Payable	6. 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. Upon entering into the 2014 Credit Facility, the Company was obligated to make monthly, interest-only payments on any term loans funded under the 2014 Credit Facility until December 1, 2014 and, thereafter, to pay 36 consecutive, equal monthly installments of principal and interest from January 1, 2015 through December 1, 2017. As per the terms of the agreement, in June 2014, upon the completion of the Company’s IPO, the term of monthly, interest-only payments were extended until June 1, 2015. Outstanding term loans under the 2014 Credit Facility bear interest at an annual rate of 8.1%. In addition, a final payment equal to 6.0% of any amounts drawn under the 2014 Credit Facility is due upon the earlier of the maturity date, acceleration of the term loans or prepayment of all or part of the term loans. The Company accrues the final payment amount due of $0.5 million, to outstanding debt by charges to interest expense using the effective-interest method from the date of issuance through the maturity date. The Company was obligated to pay a separate fee upon any IPO; a sale of substantially all of the Company’s assets; or a merger, reorganization or sale of the Company’s voting equity securities where existing voting stockholders hold less than 50% of voting equity securities after such transaction. The 2014 Credit Facility also includes events of default, the occurrence and continuation of any of which provides the lenders the right to exercise remedies against the Company and the collateral securing the loans under the 2014 Credit Facility, 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 2014 Credit Facility, insolvency, the occurrence of a material adverse event, the occurrence of any default under certain other indebtedness and a final judgment against the Company in an amount greater than $0.3 million. As of December 31, 2016 and 2015, notes payable consist of the following: December 31, 2016 (in thousands) Notes payable 3,183 Debt discount, net of accretion (9 ) Accretion related to final payment 415 Notes payable, net of discount, short term $ 3,589 December 31, 2015 (in thousands) Notes payable $ 6,119 Less: current portion (2,936 ) Notes payable, net of current portion 3,183 Debt discount, net of accretion (36 ) Accretion related to final payment 306 Notes payable, net of discount, long term $ 3,453 As of December 31, 2016, the estimated future principal payments due are as follows: Years Ending December 31, (in thousands) 2017 $ 3,183 Total $ 3,183 During the years ended December 31, 2016 2015 and 2014, the Company recognized $0.5 million, $0.8 million and $0.9 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%.

Stockholders' Equity

Stockholders' Equity	12 Months Ended
	Dec. 31, 2016
Equity [Abstract]
Stockholders' Equity	7. Stockholders’ Equity On January 28, 2015, the Company completed a follow-on follow-on follow-on As of December 31, 2016 and 2015, the Company’s Certificate of Incorporation, as amended and restated, authorizes the Company to issue 5,000,000 shares of $0.001 par value preferred stock. The rights, preferences, restrictions, qualifications and limitations of such stock are to be determined by the Company’s board of directors. As of December 31, 2016 and 2015, the Company’s Certificate of Incorporation, as amended and restated, authorizes the Company to issue 115,000,000 shares of $0.001 par value common stock.

Stock-Based Awards

Stock-Based Awards	12 Months Ended
	Dec. 31, 2016
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Stock-Based Awards	8. Stock-Based Awards Stock Option Plans The Company’s Amended and Restated 2006 Stock Option Plan (the “2006 Plan”) provided for the Company to sell or issue common stock or restricted common stock, or to grant incentive stock options or nonqualified stock options for the purchase of common stock, to employees, members of the board of directors and consultants of the Company. The 2006 Plan was administered by the board of directors, or at the discretion of the board of directors, by a committee of the board. The exercise prices, vesting and other restrictions were determined at the discretion of the board of directors, or a committee of the board of directors if so delegated, except that the exercise price per share of stock options could not be less than 100% of the fair market value of the share of common stock on the date of grant and the term of stock option could not be greater than ten years. The total number of shares of common stock that could have been issued under the 2006 Plan was 1,889,150 shares. Upon closing of the Company’s IPO, 168,221 shares reserved and not then subject to outstanding options were transferred to the 2014 Stock Option and Incentive Plan, and no further awards will be made under the 2006 Plan. On June 5, 2014, the Company’s stockholders approved the 2014 Stock Option and Incentive Plan (the “2014 Stock Option Plan”), which became effective upon the completion of the IPO of the Company’s shares of common stock in June 2014. The 2014 Stock Option 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. The number of shares initially reserved for issuance under the 2014 Stock Option Plan is 2,168,221 shares of common stock and may be increased by the number of shares under the 2006 Plan that are not needed to fulfill the Company’s obligations for awards issued under the 2006 Plan as a result of forfeiture, expiration, cancellation, termination or net issuances of awards thereunder. The number of shares of common stock that may be issued under the 2014 Stock Option Plan is also subject to increase on the first day of each fiscal year by the lesser of (i) 4% of the Company’s outstanding shares of common stock as of that date, or (ii) an amount determined by the board of directors. As of December 31, 2016, 2,107,295 shares are available for grant under the 2014 Stock Option Plan, including 1,089,700 shares automatically added to the 2014 Stock Option Plan on January 1, 2016 as a result of a provision in the 2014 Stock Option Plan. The Company generally grants stock-based awards with service conditions only (“service-based” awards). As required by the 2006 Plan and 2014 Stock Option Plan, the exercise price for stock options granted is not to be less than the fair value of common shares as of the date of grant. Prior to the IPO, the value of common stock was determined by the board of directors by taking into consideration its most recently available valuation of common shares performed by management and the board of directors as well as additional factors which might have changed since the date of the most recent contemporaneous valuation through the date of grant. During the year ended December 31, 2016, the Company granted stock options for the purchase of 1,527,559 shares of common stock, of which options for the purchase of 1,519,559 shares were granted to employees and directors and options for the purchase of 8,000 shares were granted to a consultant. During the year ended December 31, 2015, the Company granted stock options for the purchase of 992,505 shares of common stock, of which options for the purchase of 988,505 shares were granted to employees and directors and options for the purchase of 4,000 shares were granted to a consultant. 2014 Employee Stock Purchase Plan On June 5, 2014, the Company’s stockholders approved the 2014 Employee Stock Purchase Plan (the “ESPP”). A total of 265,000 shares of common stock were reserved for issuance under this plan. The ESPP became effective upon the completion of the IPO of the Company’s shares of common stock. The first offering period commenced on September 1, 2014 and ended on December 31, 2014. During both 2016 and 2015 there were two offering periods, January 1 through June 30 and July 1 through December 31. The per share purchase price for offerings is equal to the lesser of 85% of the closing market price of the Company’s common stock on the first day or last day of the offering period. The Company issued 37,663 and 7,540 shares during the years ended December 31, 2016 and 2015, respectively. As of December 31, 2016 and 2015, there are 219,797 and 257,460 shares, respectively, of common stock available for issuance to participating employees under the ESPP. Stock Option Valuation The fair value of each stock option grant is estimated on the date of grant using the Black-Scholes option-pricing model. Prior to its IPO in June 2014, the Company was a private company and lacks company-specific historical and implied volatility information. Therefore, the Company estimates its expected stock volatility based on the historical volatility of a publicly traded set of peer companies and expects to continue to do so until such time as it has adequate historical data regarding the volatility of its own traded stock price. The expected term of the Company’s stock options has been determined utilizing the “simplified” method for awards that qualify as “plain-vanilla” options. The expected term of stock options granted to nonemployees is equal to the contractual term of the option award. The risk-free interest rate is determined by reference to the U.S. Treasury yield curve in effect at the time of grant of the award for time periods approximately equal to the expected term of the award. Expected dividend yield is based on the fact that the Company has never paid cash dividends and does not expect to pay any cash dividends in the foreseeable future. The assumptions that the Company used to determine the fair value of the stock options granted to employees and directors are as follows, presented on a weighted average basis: 2016 2015 2014 Risk-free interest rate 1.40 % 1.75 % 1.90 % Expected term (in years) 6.18 6.25 6.25 Expected volatility 87 % 87 % 90 % Expected dividend yield 0 % 0 % 0 % The following table summarizes the Company’s stock option activity since December 31, 2015: Shares Issuable Weighted Average Aggregate (in years) (in thousands) Outstanding as of December 31, 2015 2,555,110 $ 19.76 Granted 1,527,559 $ 6.65 Exercised (35,000 ) $ 0.75 Forfeited (932,666 ) $ 16.90 Outstanding as of December 31, 2016 3,115,003 $ 14.40 7.2 $ 1,038 Options vested and expected to vest as of December 31, 2016 3,080,777 $ 14.40 7.2 $ 1,038 Options exercisable as of December 31, 2016 1,605,537 $ 14.18 5.5 $ 1,036 The aggregate intrinsic value of stock options is calculated as the difference between the exercise price of the stock options and the fair value of the Company’s common stock for those stock options that had exercise prices lower than the fair value of the Company’s common stock. The aggregate intrinsic value of stock options exercised was $0.1 million and $13.9 million during the years ended December 31, 2016 and 2015, respectively. The Company received cash proceeds from the exercise of stock options of less than $0.1 million and $0.8 million during the years ended December 31, 2016 and 2015, respectively. The weighted average grant-date fair value of stock options granted to employees and directors during the years ended December 31, 2016, 2015 and 2014 was $4.86, $28.97 and $11.73 per share, respectively. As of December 31, 2016 and 2015, there were outstanding unvested service-based stock options held by nonemployees for the purchase of 6,401 and 9,363 shares of common stock, respectively. Restricted Stock Awards The 2006 Plan provides for the award of restricted stock awards. The Company has granted restricted stock awards with time-based vesting conditions. Unvested shares of restricted stock awards may not be sold or transferred by the holder. These restrictions lapse according to the time-based vesting conditions of each award. The Company values restricted stock awards on the grant-date using the grant-date market price of the Company’s common stock. There were no restricted stock awards that vested in the years ended December 31, 2016, 2015 or 2014. The aggregate intrinsic value of restricted stock awards is calculated as the fair value of the Company’s common stock on the date it vests and is released. The Company did not grant any restricted stock awards during the years ended December 31, 2016, 2015 or 2014. As of December 31, 2016, 2015 and 2014, there were no unvested restricted stock awards subject to repurchase. Restricted Stock Units The 2014 Stock Option Plan provides for the award of restricted stock units. The Company has granted restricted stock units with time-based vesting conditions. The restrictions lapse according to the time based vesting conditions of each award. The Company values restricted stock units on the grant-date using the grant-date market price of the Company’s common stock. The aggregate intrinsic value of restricted stock units that vested during the years ended December 31, 2016 and 2015 was $0.1 million. There were no restricted stock units that vested in the year ended December 31, 2014. The aggregate intrinsic value of restricted stock units is calculated as the fair value of the Company’s common stock on the date it vests and is released. During the years ended December 31, 2016 and 2015, the Company granted 13,273 and 4,769 restricted stock units, all of which vested during 2016 and 2015, respectively, at a weighted average grant-date fair value of $7.91 and $34.46, respectively. The Company did not grant any restricted stock units during the year ended December 31, 2014. As of December 31, 2016, 2015 and 2014, there were no unvested restricted stock units outstanding. Stock-based Compensation The Company recorded stock-based compensation expense related to stock options and restricted common stock in the following expense categories within its consolidated statements of operations: Year Ended December 31, 2016 2015 2014 (in thousands) Research and development $ 3,543 $ 2,930 $ 490 General and administrative 6,390 5,652 1,063 $ 9,933 $ 8,582 $ 1,553 In addition, during the year ended December 31, 2016, in connection with its strategic restructuring further discussed in Note 14, the Company recorded a one-time, non-cash As of December 31, 2016, the Company had an aggregate of $14.1 million of unrecognized stock-based compensation cost, which is expected to be recognized over a weighted average period of 2.2 years.

Net Loss Per Share

Net Loss Per Share	12 Months Ended
	Dec. 31, 2016
Earnings Per Share [Abstract]
Net Loss Per Share	9. Net Loss Per Share Basic and diluted net loss per share attributable to common stockholders was calculated as follows: Year Ended December 31, 2016 2015 2014 (in thousands, except per share data) Basic and diluted net loss per share attributable to common stockholders: Numerator: Net loss $ (57,878 ) $ (74,286 ) $ (36,478 ) Accretion of redeemable convertible preferred stock to redemption value — — (92 ) Net loss attributable to common stockholders $ (57,878 ) $ (74,286 ) $ (36,570 ) Denominator: Weighted average common shares outstanding, basic and diluted 27,297,934 26,756,079 12,189,155 Net loss per share attributable to common stockholders, basic and diluted $ (2.12 ) $ (2.78 ) $ (3.00 ) The Company excluded the following common stock equivalents, outstanding as of December 31, 2016, 2015 and 2014, from the computation of diluted net loss per share attributable to common stockholders for the years ended December 31, 2016, 2015 and 2014 because they had an anti-dilutive impact due to the net loss attributable to common stockholders incurred for the periods: As of December 31, 2016 2015 2014 Options to purchase common stock 3,115,003 2,555,110 2,008,574

Commitments and Contingencies

Commitments and Contingencies	12 Months Ended
	Dec. 31, 2016
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	10. Commitments and Contingencies Leases The Company has a lease for office space in Boston, Massachusetts, effective as of July 28, 2014, with a term expiring July 31, 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 a 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 is currently in negotiations regarding the financial terms of these extensions. In addition, with the landlord’s consent, the Company have subleased 2,976 square feet of office space in Boston, Massachusetts to an unrelated third party beginning on January 1, 2017 and expiring on December 31, 2017, and the Company expects to receive approximately $0.1 million in sublease rental income. Future minimum lease payments for its operating leases as of December 31, 2016 were as follows: Years Ending December 31, (in thousands) 2017 $ 300 2018 106 2019 82 $ 488 During the years ended December 31, 2016, 2015 and 2014, the Company recognized $0.4 million, $0.3 million and $0.2 million, respectively, of rental expense related to office space. Intellectual Property Licenses The Company has acquired exclusive rights to develop patented compounds and related know-how Year Ended December 31, 2016 2015 2014 (in thousands) License, milestone, and license maintenance fees $ — $ — $ 7,019 $ — $ — $ 7,019 As of December 31, 2016, 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 years ended December 31, 2016 or 2015. During the year ended December 31, 2014, the Company recorded expenses of $7.0 million relating to milestones achieved in September 2014 upon the initiation of a first Phase 3 clinical trial including the cost of the issuance of common stock valued at $3.6 million. The Company is also obligated to pay to the licensors a percentage of fees received if and when the Company sublicenses the technology. As of December 31, 2016, the Company has not yet developed a commercial product using the licensed technologies and it has not entered into any sublicense agreements for the technologies. Indemnification Agreements In the ordinary course of business, the Company may provide indemnification of varying scope and terms to vendors, lessors, business partners, and other parties with respect to certain matters including, but not limited to, losses arising out of breach of such agreements or from intellectual property infringement claims made by third parties. In addition, the Company has entered into indemnification agreements with members of management team and the board of directors of the Company that will require the Company, among other things, to indemnify them against certain liabilities that may arise by reason of their status or service as directors or officers. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is, in many cases, unlimited. To date, the Company has not incurred any material costs as a result of such indemnifications. The Company does not believe that the outcome of any claims under indemnification arrangements will have a material effect on its financial position, results of operations or cash flows, and it has not accrued any liabilities related to such obligations in its consolidated financial statements as of December 31, 2016. 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. Other than the above action, the Company is not aware of any other material claims as of December 31, 2016.

Income Taxes

Income Taxes	12 Months Ended
	Dec. 31, 2016
Income Tax Disclosure [Abstract]
Income Taxes	11. Income Taxes During the years ended December 31, 2016, 2015 and 2014, the Company recorded no income tax benefits for the net operating losses incurred in each year due to its uncertainty of realizing a benefit from those items. The domestic and foreign components of loss before income taxes are as follows: 2016 2015 2014 (in thousands) Domestic $ (57,799 ) $ (72,147 ) $ (35,818 ) Foreign (79 ) (2,139 ) (660 ) Loss before income taxes $ (57,878 ) $ (74,286 ) $ (36,478 ) A reconciliation of the U.S. federal statutory income tax rate to the Company’s effective income tax rate is as follows: Year Ended December 31, 2016 2015 2014 Federal statutory income tax rate (34.0 %) (34.0 %) (34.0 %) Federal and state research and development tax credit (2.9 ) (3.9 ) (1.9 ) State taxes, net of federal benefit (3.9 ) (3.9 ) (4.0 ) Orphan drug tax credit (1.3 ) (3.5 ) (3.2 ) Stock compensation expense 0.7 0.9 0.6 Nondeductible Australia research and development expenses 0.0 1.0 0.6 Other items 1.3 0.1 2.4 Change in deferred tax asset valuation allowance 40.1 43.3 39.5 Effective income tax rate 0.0 % 0.0 % 0.0 % Net deferred tax assets as of December 31, 2016 and 2015 consisted of the following: December 31, 2016 2015 (in thousands) Noncurrent deferred tax assets: Capitalized research and development expenses 59,489 46,568 Net operating loss carryforwards 14,991 11,186 Tax credit carryforwards 14,297 11,570 Capitalized legal expenses 2,119 1,773 Stock-based compensation 6,027 2,780 Accrued expenses 783 648 Other temporary differences 14 16 Total noncurrent deferred tax assets 97,720 74,541 Total gross deferred tax assets 97,720 74,541 Valuation allowance (97,720 ) (74,541 ) Net deferred tax assets $ — $ — Changes in the valuation allowance for deferred tax assets during the years ended December 31, 2016, 2015 and 2014 related primarily to the increase in net operating loss carryforwards, capitalized research and development expenses and tax credit carryforwards and were as follows: Year Ended December 31, 2016 2015 2014 (in thousands) Valuation allowance as of beginning of year $ 74,541 $ 42,398 $ 27,831 Decreases recorded as benefit to income tax provision — — — Increases recorded to income tax provision 23,179 32,143 14,567 Valuation allowance as of end of year $ 97,720 $ 74,541 $ 42,398 As of December 31, 2016, the Company had net operating loss carryforwards for federal and state income tax purposes of $49.1 million and $35.9 million, respectively, which begin to expire in 2026 and 2030, respectively. As of December 31, 2016, the Company did not record deferred tax assets of $12.8 million (gross) that were attributable to stock option exercises which will be recorded as an increase in additional paid in capital once they are realized in accordance with accounting for stock-based compensation awards. These deductions are not reflected in the federal and state net operating loss carryforwards and the capitalized research and development expense deferred tax assets in the amounts of $9.4 million, $7.2 million, and $3.4 million, respectively. As of December 31, 2016, the Company also had available tax credit carryforwards for federal and state income tax purposes of $13.1 million and $1.9 million, respectively, which begin to expire in 2026 and 2021, respectively. Utilization of the net operating loss carryforwards and tax credit carryforwards may be subject to a substantial annual limitation under Section 382 of the Internal Revenue Code of 1986 due to ownership changes that have occurred previously or that could occur in the future. These ownership changes may limit the amount of carryforwards that can be utilized annually to offset future taxable income. In general, an ownership change, as defined by Section 382, results from transactions increasing the ownership of certain stockholders or public groups in the stock of a corporation by more than 50% over a three-year period. The Company has not conducted a study to assess whether a change of control has occurred or whether there have been multiple changes of control since inception due to the significant complexity and cost associated with such a study. If the Company has experienced a change of control, as defined by Section 382, at any time since inception, utilization of the net operating loss carryforwards or tax credit carryforwards would be subject to an annual limitation under Section 382, which is determined by first multiplying the value of the Company’s stock at the time of the ownership change by the applicable long-term tax-exempt As of December 31, 2016 and 2015, the Company’s gross deferred tax asset balance of $97.7 million and $74.5 million, respectively, was comprised principally of net operating loss carryforwards, capitalized research and development expenses and tax credit carryforwards. During the years ended December 31, 2016, 2015 and 2014, gross deferred tax assets increased due to additional net operating loss carryforwards, research and development tax credits generated and additional research and development expenses capitalized for tax purposes. The Company has evaluated the positive and negative evidence bearing upon its ability to realize the deferred tax assets. Management has considered the Company’s history of cumulative net losses incurred since inception and its lack of commercialization of any products or generation of any revenue from product sales since inception and has concluded that it is more likely than not that the Company will not realize the benefits of the deferred tax assets. Accordingly, a full valuation allowance has been established against the deferred tax assets as of December 31, 2016 and 2015. Management reevaluates the positive and negative evidence at each reporting period. The Company has not recorded any amounts for unrecognized tax benefits as of December 31, 2016 or 2015. The Company files tax returns as prescribed by the tax laws of the jurisdictions in which it operates. In the normal course of business, the Company is subject to examination by federal and state jurisdictions, where applicable. There are currently no pending income tax examinations. The Company’s tax years are still open under statute from 2013 to the present for federal income tax purposes and from 2012 to the present for state purposes. Earlier years may be examined to the extent that tax credit or net operating loss carryforwards are used in future periods. The Company’s policy is to record interest and penalties related to income taxes as part of its income tax provision. The Company considers only the direct effects of windfall tax deductions. The deferred tax assets above exclude $9.4 million and $7.2 million of gross ($3.2 million and $0.4 million tax effected) federal and state net operating losses, respectively, and $3.4 million of gross ($1.3 million tax effected) capitalized research and development related to tax deductions from the exercise of stock options subsequent to the adoption of the 2006 accounting standard on stock-based compensation. This amount represents an excess tax benefit and has not been included in the gross deferred tax assets. The Company will adopt ASU No. 2016-09, Improvements to Employee Share-Based Payment Accounting No. 2016-09

Retirement Plan

Retirement Plan	12 Months Ended
	Dec. 31, 2016
Compensation and Retirement Disclosure [Abstract]
Retirement Plan	12. 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 years ended December 31, 2016, 2015 and 2014, the Company recognized $0.2 million, $0.1 million and less than $0.1 million, respectively, of expense related to its contributions to the plan.

Australia Research and Developm

Australia Research and Development Tax Incentive	12 Months Ended
	Dec. 31, 2016
Research and Development [Abstract]
Australia Research and Development Tax Incentive	13. Australia Research and Development Tax Incentive The Company’s wholly owned subsidiary, Zafgen Australia Pty Limited, which conducts core research and development activities on behalf of the Company, is eligible to receive a 45% refundable tax incentive for qualified research and development activities. For the years ended December 31, 2016, 2015 and 2014, $0.3 million, $1.4 million and $0.4 million, respectively, were recorded as a reduction to research and development expenses in the consolidated statements of operations. These amounts represented 45% of the Company’s qualified research and development spending in Australia. The refund is denominated in Australian dollars and, therefore, the related receivable is re-measured

Restructuring

Restructuring	12 Months Ended
	Dec. 31, 2016
Restructuring and Related Activities [Abstract]
Restructuring	14. Restructuring On July 19, 2016, the Company announced that following a comprehensive review of its assets and clinical programs, as well as feedback from regulatory authorities, the Company refocused its resources on development of a differentiated second-generation MetAP2 inhibitor, ZGN-1061. ZGN-1061 During the year ended December 31, 2016, the Company recorded $1.4 million of restructuring-related costs in operating expense, including employee severance, benefits and related costs, as well as a stock option modification. The stock option modification was a one-time, non-cash The following table summarizes the restructuring costs by category for the periods indicated: Year Ended December 31, 2016 (in thousands) Cash Non-cash Total Research and development $ 455 $ 7 $ 462 General and administrative 768 173 941 $ 1,223 $ 180 $ 1,403 The following table summarizes the restructuring reserve for the periods indicated: Year Ended December 31, 2016 (in thousands) Restructuring reserve beginning balance $ — Restructuring expenses incurred during the period 1,223 Amounts paid during the period (847 ) Restructuring reserve ending balance $ 376

Quarterly Financial Data (Unaud

Quarterly Financial Data (Unaudited)	12 Months Ended
	Dec. 31, 2016
Quarterly Financial Information Disclosure [Abstract]
Quarterly Financial Data (Unaudited)	15. Quarterly Financial Data (Unaudited) The following information has been derived from unaudited consolidated financial statements that, in the opinion of management, include all recurring adjustments necessary for a fair statement of such information. Three Months Ended March 31, June 30, September 30, December 31, 2016 2016 2016 2016 (in thousands, except per share data) Revenue $ — $ — $ — $ — Operating expenses 17,857 15,062 14,831 10,475 Net loss (17,736 ) (15,028 ) (14,675 ) (10,439 ) Net loss per share, basic and diluted $ (0.65 ) $ (0.55 ) $ (0.54 ) $ (0.38 ) Weighted average common shares outstanding, basic and diluted 27,263,435 27,272,225 27,322,907 27,332,515 Three Months Ended March 31, June 30, September 30, December 31, 2015 2015 2015 2015 (in thousands, except per share data) Revenue $ — $ — $ — $ — Operating expenses 13,240 17,610 19,717 23,246 Net loss (13,472 ) (17,756 ) (19,884 ) (23,174 ) Net loss per share, basic and diluted $ (0.53 ) $ (0.66 ) $ (0.73 ) $ (0.85 ) Weighted average common shares outstanding, basic and diluted 25,615,282 27,011,960 27,138,667 27,238,079

Summary of Significant Accoun23

Summary of Significant Accounting Policies (Policies)	12 Months Ended
	Dec. 31, 2016
Accounting Policies [Abstract]
Use of Estimates	Use of Estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities as of the date of the consolidated financial statements, and the reported amounts of expenses during the reporting periods. Significant estimates and assumptions reflected in these consolidated financial statements include, but are not limited to, the accrual of research and development expenses and the valuation of stock-based awards. Estimates are periodically reviewed in light of changes in circumstances, facts and experience. Actual results could differ from the Company’s estimates.
Cash Equivalents	Cash Equivalents The Company considers all short-term, highly liquid investments with original maturities of ninety days or less at acquisition date to be cash equivalents. Cash equivalents, which consist of money market funds, U.S. government securities, corporate bonds, and commercial paper, are stated at fair value.
Concentration of Credit Risk and of Significant Suppliers	Concentration of Credit Risk and of Significant Suppliers Financial instruments that potentially expose the Company to concentrations of credit risk consist primarily of cash, cash equivalents and marketable securities. The Company has all cash, cash equivalents and marketable securities balances at two accredited financial institutions in amounts that exceed federally insured limits. The Company does not believe that it is subject to unusual credit risk beyond the normal credit risk associated with commercial banking relationships. The Company is dependent on third-party manufacturers to supply products for research and development activities in its programs. In particular, the Company relies and expects to continue to rely on a small number of manufacturers to supply it with its requirements for the active pharmaceutical ingredients and formulated drugs related to these programs. These programs could be adversely affected by a significant interruption in the supply of active pharmaceutical ingredients and formulated drugs.
Marketable securities	Marketable securities Marketable securities consist of investments with original maturities greater than ninety days. The Company has classified its investments with maturities beyond one year as short term, based on their highly liquid nature and because such marketable securities represent the investment of cash that is available for current operations. The Company considers its investment portfolio of investments as available-for-sale.
Deferred Offering Costs	Deferred Offering Costs The Company capitalizes certain legal, accounting and other third-party fees that are directly associated with in-process paid-in
Property and Equipment	Property and Equipment Property and equipment are stated at cost less accumulated depreciation. Depreciation expense is recognized using the straight-line method over a five-year estimated useful life for equipment, furniture and fixtures and office equipment. Leasehold improvements are amortized over the shorter of the asset life or the term of the lease agreement. Expenditures for repairs and maintenance of assets are charged to expense as incurred. Upon retirement or sale, the cost and related accumulated depreciation of assets disposed of are removed from the accounts and any resulting gain or loss is included in loss from operations.
Impairment of Long-Lived Assets	Impairment of Long-Lived Assets Long-lived assets consist of property and equipment. Long-lived assets to be held and used are tested for recoverability whenever events or changes in business circumstances indicate that the carrying amount of the assets may not be fully recoverable. Factors that the Company considers in deciding when to perform an impairment review include significant underperformance of the business in relation to expectations, significant negative industry or economic trends, and significant changes or planned changes in the use of the assets. If an impairment review is performed to evaluate a long-lived asset for recoverability, the Company compares forecasts of undiscounted cash flows expected to result from the use and eventual disposition of the long-lived asset to its carrying value. An impairment loss would be recognized when estimated undiscounted future cash flows expected to result from the use of an asset are less than its carrying amount. The impairment loss would be based on the excess of the carrying value of the impaired asset over its fair value, determined based on discounted cash flows. To date, the Company has not recorded any impairment losses on long-lived assets.
Research and Development Costs	Research and Development Costs Research and development costs are expensed as incurred. Included in research and development expenses are wages, stock-based compensation and benefits of employees, third-party license fees and milestones and other operational costs related to the Company’s research and development activities, including facility-related expenses and external costs of outside vendors engaged to conduct pre-clinical
Research Contract Costs and Accruals	Research Contract Costs and Accruals The Company has entered into various research and development contracts with research institutions and other companies both inside and outside of the United States. These agreements are generally cancelable, and related payments are recorded as research and development expenses as incurred. The Company records accruals for estimated ongoing research costs. When evaluating the adequacy of the accrued liabilities, the Company analyzes progress of the studies, including the phase or completion of events, invoices received and contracted costs. Significant judgments and estimates are made in determining the accrued balances at the end of any reporting period. Actual results could differ from the Company’s estimates. The Company’s historical accrual estimates have not been materially different from the actual costs.
Patent Costs	Patent Costs All patent-related costs incurred in connection with filing and prosecuting patent applications are recorded as general and administrative expenses as incurred, as recoverability of such expenditures is uncertain.
Accounting for Stock-Based Compensation	Accounting for Stock-Based Compensation The Company measures all stock options and other stock-based awards granted to employees and directors at the fair value on the date of the grant using the Black-Scholes option-pricing model. The fair value of the awards is recognized as expense, net of estimated forfeitures, over the requisite service period, which is generally the vesting period of the respective award. The straight-line method of expense recognition is applied to all awards with service-only conditions. For stock-based awards granted to consultants and nonemployees, compensation expense is recognized over the period during which services are rendered by such consultants and nonemployees until completed. At the end of each financial reporting period prior to completion of the service, the fair value of these awards is re-measured The Company classifies stock-based compensation expense in its consolidated statement of operations and comprehensive loss in the same manner in which the award recipient’s payroll costs are classified or in which the award recipients’ service payments are classified. The Company recognizes compensation expense for only the portion of awards that are expected to vest. In developing a forfeiture rate estimate, the Company has considered its historical experience to estimate pre-vesting
Income Taxes	Income Taxes The Company accounts for income taxes using the asset and liability method, which requires the recognition of deferred tax assets and liabilities for the expected future tax consequences of events that have been recognized in the consolidated financial statements or in the Company’s tax returns. Deferred taxes are determined based on the difference between the financial statement and tax basis of assets and liabilities using enacted tax rates in effect in the years in which the differences are expected to reverse. Changes in deferred tax assets and liabilities are recorded in the provision for income taxes. The Company assesses the likelihood that its deferred tax assets will be recovered from future taxable income and, to the extent it believes, based upon the weight of available evidence, that it is more likely than not that all or a portion of deferred tax assets will not be realized, a valuation allowance is established through a charge to income tax expense. Potential for recovery of deferred tax assets is evaluated by estimating the future taxable profits expected and considering prudent and feasible tax planning strategies. The Company accounts for uncertainty in income taxes recognized in the consolidated financial statements by applying a two-step more-likely-than-not
Segment Data	Segment Data The Company manages its operations as a single segment for the purposes of assessing performance and making operating decisions. The Company’s singular focus is on advancing novel therapeutics for patients suffering from type 2 diabetes, severe obesity and obesity-related disorders. No revenue has been generated since inception, and all tangible assets are held in the United States.
Comprehensive Loss	Comprehensive Loss Comprehensive loss includes net loss as well as other changes in stockholders’ equity (deficit) that result from transactions and economic events other than those with stockholders. For the years ended December 31, 2016, 2015 and 2014, the Company’s only element of other comprehensive loss was unrealized gain or loss on marketable securities.
Net Income (Loss) Per Share	Net Income (Loss) Per Share Upon the closing of the Company’s IPO in June 2014, all of the Company’s outstanding redeemable convertible preferred shares were converted into shares of common stock. Prior to this conversion, the Company followed the two-class two-class two-class two-class 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.
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 2016-08 , Revenue from Contract with Customers: Principal versus Agent Considerations 2016-10, Revenue from Contracts with Customers: Identifying Performance Obligations and Licensing 2016-12, Revenue from Contracts with Customers: Narrow-Scope Improvements and Practical Expedients. non-cash In August 2014, the FASB issued ASU No. 2014-15, Presentation of Financial Statements—Going Concern In November 2015, the FASB issued ASU No. 2015-17, Balance Sheet Classification of Deferred Taxes. 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 In August 2016, the FASB issued ASU No. 2016-15, Statement of Cash Flows: Classification of Certain Cash Receipts and Cash Payments
Reclassifications	Reclassifications Prior period financial statement amounts have been reclassified to conform to current period presentation.

Fair Value Measurements and M24

Fair Value Measurements and Marketable Securities (Tables)	12 Months Ended
	Dec. 31, 2016
Fair Value Disclosures [Abstract]
Summary of Cash Equivalents and Marketable Securities	The following tables summarize the Company’s cash equivalents and marketable securities as of December 31, 2016 and 2015: 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 $ — December 31, 2015 Total Quoted Significant Significant (in thousands) Cash equivalents: Money market funds $ 13,231 $ 13,231 $ — $ — U.S. government securities 4,999 — 4,999 — Commercial paper 4,697 — 4,697 — Corporate bonds 3,000 — 3,000 — Total cash equivalents 25,927 13,231 12,696 — Marketable securities: Corporate bonds 125,516 — 125,516 — Commercial paper 19,468 — 19,468 — U.S. government securities 4,500 — 4,500 — Total marketable securities 149,484 — 149,484 — Total cash equivalents and marketable securities $ 175,411 $ 13,231 $ 162,180 $ —
Summary of Marketable Securities	The following tables summarize the Company’s marketable securities as of December 31, 2016 and 2015: December 31, 2016 Amortized Gross Gross Fair Value (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 December 31, 2015 Amortized Gross Gross Fair Value (in thousands) Assets: Corporate bonds (due within 1 year) $ 112,828 $ 1 $ (169 ) $ 112,660 Corporate bonds (due after 1 year through 2 years) 12,885 3 (32 ) 12,856 Commercial paper (due within 1 year) 19,478 — (10 ) 19,468 U.S. government securities (due within 1 year) 4,500 — — 4,500 $ 149,691 $ 4 $ (211 ) $ 149,484

Property and Equipment, net (Ta

Property and Equipment, net (Tables)	12 Months Ended
	Dec. 31, 2016
Property, Plant and Equipment [Abstract]
Schedule of Property Plant and Equipment Net	Property and equipment, net consisted of the following as of December 31, 2016 and 2015: December 31, Useful Life 2016 2015 (in thousands) Office equipment 5 years $ 372 $ 359 Furniture and fixtures 5 years 194 186 Equipment 5 years — 71 Leasehold improvements * 415 406 981 1,022 Less: Accumulated depreciation (320 ) (120 ) $ 661 $ 902 * shorter of asset life or lease term

Accrued Expenses (Tables)

Accrued Expenses (Tables)	12 Months Ended
	Dec. 31, 2016
Payables and Accruals [Abstract]
Schedule of Accrued Expenses	Accrued expenses consisted of the following as of December 31, 2016 and 2015: December 31, 2016 2015 (in thousands) Accrued payroll and related expenses $ 2,008 $ 1,802 Accrued research and development expenses 892 3,727 Accrued restructuring 376 — Accrued professional fees 347 422 Accrued other 110 161 $ 3,733 $ 6,112

Notes Payable (Tables)

Notes Payable (Tables)	12 Months Ended
	Dec. 31, 2016
Debt Disclosure [Abstract]
Schedule of Notes Payable	As of December 31, 2016 and 2015, notes payable consist of the following: December 31, 2016 (in thousands) Notes payable 3,183 Debt discount, net of accretion (9 ) Accretion related to final payment 415 Notes payable, net of discount, short term $ 3,589 December 31, 2015 (in thousands) Notes payable $ 6,119 Less: current portion (2,936 ) Notes payable, net of current portion 3,183 Debt discount, net of accretion (36 ) Accretion related to final payment 306 Notes payable, net of discount, long term $ 3,453
Schedule of Estimated Future Principal Payments	As of December 31, 2016, the estimated future principal payments due are as follows: Years Ending December 31, (in thousands) 2017 $ 3,183 Total $ 3,183

Stock-Based Awards (Tables)

Stock-Based Awards (Tables)	12 Months Ended
	Dec. 31, 2016
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Assumptions used to Determine Fair Value of Stock Options Granted	The assumptions that the Company used to determine the fair value of the stock options granted to employees and directors are as follows, presented on a weighted average basis: 2016 2015 2014 Risk-free interest rate 1.40 % 1.75 % 1.90 % Expected term (in years) 6.18 6.25 6.25 Expected volatility 87 % 87 % 90 % Expected dividend yield 0 % 0 % 0 %
Summary of Stock Option Activity	The following table summarizes the Company’s stock option activity since December 31, 2015: Shares Issuable Weighted Average Aggregate (in years) (in thousands) Outstanding as of December 31, 2015 2,555,110 $ 19.76 Granted 1,527,559 $ 6.65 Exercised (35,000 ) $ 0.75 Forfeited (932,666 ) $ 16.90 Outstanding as of December 31, 2016 3,115,003 $ 14.40 7.2 $ 1,038 Options vested and expected to vest as of December 31, 2016 3,080,777 $ 14.40 7.2 $ 1,038 Options exercisable as of December 31, 2016 1,605,537 $ 14.18 5.5 $ 1,036
Summary of Stock-Based Compensation Expense Related to Stock Options and Restricted Common Stock	The Company recorded stock-based compensation expense related to stock options and restricted common stock in the following expense categories within its consolidated statements of operations: Year Ended December 31, 2016 2015 2014 (in thousands) Research and development $ 3,543 $ 2,930 $ 490 General and administrative 6,390 5,652 1,063 $ 9,933 $ 8,582 $ 1,553

Net Loss Per Share (Tables)

Net Loss Per Share (Tables)	12 Months Ended
	Dec. 31, 2016
Earnings Per Share [Abstract]
Computation of Basic and Diluted Earnings Per Share	Basic and diluted net loss per share attributable to common stockholders was calculated as follows: Year Ended December 31, 2016 2015 2014 (in thousands, except per share data) Basic and diluted net loss per share attributable to common stockholders: Numerator: Net loss $ (57,878 ) $ (74,286 ) $ (36,478 ) Accretion of redeemable convertible preferred stock to redemption value — — (92 ) Net loss attributable to common stockholders $ (57,878 ) $ (74,286 ) $ (36,570 ) Denominator: Weighted average common shares outstanding, basic and diluted 27,297,934 26,756,079 12,189,155 Net loss per share attributable to common stockholders, basic and diluted $ (2.12 ) $ (2.78 ) $ (3.00 )
Summary of Common Stock Equivalents Outstanding	The Company excluded the following common stock equivalents, outstanding as of December 31, 2016, 2015 and 2014, from the computation of diluted net loss per share attributable to common stockholders for the years ended December 31, 2016, 2015 and 2014 because they had an anti-dilutive impact due to the net loss attributable to common stockholders incurred for the periods: As of December 31, 2016 2015 2014 Options to purchase common stock 3,115,003 2,555,110 2,008,574

Commitments and Contingencies (

Commitments and Contingencies (Tables)	12 Months Ended
	Dec. 31, 2016
Commitments and Contingencies Disclosure [Abstract]
Schedule of Future Minimum Lease Payments for Operating Leases	Future minimum lease payments for its operating leases as of December 31, 2016 were as follows: Years Ending December 31, (in thousands) 2017 $ 300 2018 106 2019 82 $ 488
Research and Development Expenses Related to License Agreements	Related to these license agreements, the Company recorded research and development expenses in its consolidated statements of operations as follows: Year Ended December 31, 2016 2015 2014 (in thousands) License, milestone, and license maintenance fees $ — $ — $ 7,019 $ — $ — $ 7,019

Income Taxes (Tables)

Income Taxes (Tables)	12 Months Ended
	Dec. 31, 2016
Income Tax Disclosure [Abstract]
Schedule of Domestic and Foreign Components of Loss Before Income Taxes	The domestic and foreign components of loss before income taxes are as follows: 2016 2015 2014 (in thousands) Domestic $ (57,799 ) $ (72,147 ) $ (35,818 ) Foreign (79 ) (2,139 ) (660 ) Loss before income taxes $ (57,878 ) $ (74,286 ) $ (36,478 )
Reconciliation of Federal Statutory Income Tax Rate	A reconciliation of the U.S. federal statutory income tax rate to the Company’s effective income tax rate is as follows: Year Ended December 31, 2016 2015 2014 Federal statutory income tax rate (34.0 %) (34.0 %) (34.0 %) Federal and state research and development tax credit (2.9 ) (3.9 ) (1.9 ) State taxes, net of federal benefit (3.9 ) (3.9 ) (4.0 ) Orphan drug tax credit (1.3 ) (3.5 ) (3.2 ) Stock compensation expense 0.7 0.9 0.6 Nondeductible Australia research and development expenses 0.0 1.0 0.6 Other items 1.3 0.1 2.4 Change in deferred tax asset valuation allowance 40.1 43.3 39.5 Effective income tax rate 0.0 % 0.0 % 0.0 %
Schedule of Net Deferred Tax Assets	Net deferred tax assets as of December 31, 2016 and 2015 consisted of the following: December 31, 2016 2015 (in thousands) Noncurrent deferred tax assets: Capitalized research and development expenses 59,489 46,568 Net operating loss carryforwards 14,991 11,186 Tax credit carryforwards 14,297 11,570 Capitalized legal expenses 2,119 1,773 Stock-based compensation 6,027 2,780 Accrued expenses 783 648 Other temporary differences 14 16 Total noncurrent deferred tax assets 97,720 74,541 Total gross deferred tax assets 97,720 74,541 Valuation allowance (97,720 ) (74,541 ) Net deferred tax assets $ — $ —
Summary Changes in the Valuation Allowance for Deferred Tax Assets	Changes in the valuation allowance for deferred tax assets during the years ended December 31, 2016, 2015 and 2014 related primarily to the increase in net operating loss carryforwards, capitalized research and development expenses and tax credit carryforwards and were as follows: Year Ended December 31, 2016 2015 2014 (in thousands) Valuation allowance as of beginning of year $ 74,541 $ 42,398 $ 27,831 Decreases recorded as benefit to income tax provision — — — Increases recorded to income tax provision 23,179 32,143 14,567 Valuation allowance as of end of year $ 97,720 $ 74,541 $ 42,398

Restructuring (Tables)

Restructuring (Tables)	12 Months Ended
	Dec. 31, 2016
Restructuring and Related Activities [Abstract]
Summary of Restructuring Costs by Category	The following table summarizes the restructuring costs by category for the periods indicated: Year Ended December 31, 2016 (in thousands) Cash Non-cash Total Research and development $ 455 $ 7 $ 462 General and administrative 768 173 941 $ 1,223 $ 180 $ 1,403
Summary of Restructuring Reserve	The following table summarizes the restructuring reserve for the periods indicated: Year Ended December 31, 2016 (in thousands) Restructuring reserve beginning balance $ — Restructuring expenses incurred during the period 1,223 Amounts paid during the period (847 ) Restructuring reserve ending balance $ 376

Quarterly Financial Data (Una33

Quarterly Financial Data (Unaudited) (Tables)	12 Months Ended
	Dec. 31, 2016
Quarterly Financial Information Disclosure [Abstract]
Schedule of Unaudited Consolidated Financial Statements	The following information has been derived from unaudited consolidated financial statements that, in the opinion of management, include all recurring adjustments necessary for a fair statement of such information. Three Months Ended March 31, June 30, September 30, December 31, 2016 2016 2016 2016 (in thousands, except per share data) Revenue $ — $ — $ — $ — Operating expenses 17,857 15,062 14,831 10,475 Net loss (17,736 ) (15,028 ) (14,675 ) (10,439 ) Net loss per share, basic and diluted $ (0.65 ) $ (0.55 ) $ (0.54 ) $ (0.38 ) Weighted average common shares outstanding, basic and diluted 27,263,435 27,272,225 27,322,907 27,332,515 Three Months Ended March 31, June 30, September 30, December 31, 2015 2015 2015 2015 (in thousands, except per share data) Revenue $ — $ — $ — $ — Operating expenses 13,240 17,610 19,717 23,246 Net loss (13,472 ) (17,756 ) (19,884 ) (23,174 ) Net loss per share, basic and diluted $ (0.53 ) $ (0.66 ) $ (0.73 ) $ (0.85 ) Weighted average common shares outstanding, basic and diluted 25,615,282 27,011,960 27,138,667 27,238,079

Nature of the Business and Ba34

Nature of the Business and Basis of Presentation - Additional Information (Detail) - USD ($) $ in Thousands	1 Months Ended	12 Months Ended	133 Months Ended
	Dec. 31, 2016	Dec. 31, 2016	Dec. 31, 2016	Dec. 31, 2015
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Entity incorporation date		Nov. 22, 2005
Percentage of workforce reduction	31.00%
Accumulated deficit	$ (237,549)	$ (237,549)	$ (237,549)	$ (179,671)
Net proceeds from sale of securities			333,300
Total cash, cash equivalents and marketable securities	$ 129,200	$ 129,200	$ 129,200

Summary of Significant Accoun35

Summary of Significant Accounting Policies - Additional Information (Detail)	12 Months Ended
	Dec. 31, 2016USD ($)
Accounting Policies [Abstract]
Estimated useful life	5 years
Impairment losses on long-lived assets	$ 0
Percentage of likelihood to be realized upon ultimate settlement, description	50.00%

Fair Value Measurements and M36

Fair Value Measurements and Marketable Securities - Summary of Cash Equivalents and Marketable Securities (Detail) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	$ 26,588	$ 25,927
Marketable securities	96,842	149,484
Total cash equivalents and marketable securities	123,430	175,411
Money Market Funds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	22,091	13,231
U.S. Government Securities [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents		4,999
Marketable securities		4,500
Corporate Bonds [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	1,500	3,000
Marketable securities	69,622	125,516
Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	2,997	4,697
Marketable securities	27,220	19,468
Quoted Prices in Active Markets, (Level 1) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	22,091	13,231
Total cash equivalents and marketable securities	22,091	13,231
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	22,091	13,231
Significant Other Observable Inputs (Level 2) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	4,497	12,696
Marketable securities	96,842	149,484
Total cash equivalents and marketable securities	101,339	162,180
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		4,999
Marketable securities		4,500
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	3,000
Marketable securities	69,622	125,516
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	2,997	4,697
Marketable securities	$ 27,220	$ 19,468

Fair Value Measurements and M37

Fair Value Measurements and Marketable Securities - Summary of Marketable Securities (Detail) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 96,922	$ 149,691
Gross Unrealized Gains		4
Gross Unrealized Losses	(80)	(211)
Fair Value	96,842	149,484
Corporate Bonds (Due within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	68,777	112,828
Gross Unrealized Gains		1
Gross Unrealized Losses	(54)	(169)
Fair Value	68,723	112,660
Corporate Bonds (Due After 1 Year Through 2 Years) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	901	12,885
Gross Unrealized Gains		3
Gross Unrealized Losses	(2)	(32)
Fair Value	899	12,856
Commercial Paper (Due within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	27,244	19,478
Gross Unrealized Losses	(24)	(10)
Fair Value	$ 27,220	19,468
U.S. Government Securities (Due within 1 Year) [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost		4,500
Fair Value		$ 4,500

Property and Equipment, Net - S

Property and Equipment, Net - Schedule of Property Plant and Equipment Net (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015
Property, Plant and Equipment [Line Items]
Property and equipment, Useful Life	5 years
Property and equipment, gross	$ 981	$ 1,022
Less: Accumulated depreciation	(320)	(120)
Property and equipment, net	$ 661	902
Office Equipment [Member]
Property, Plant and Equipment [Line Items]
Property and equipment, Useful Life	5 years
Property and equipment, gross	$ 372	359
Furniture and Fixtures [Member]
Property, Plant and Equipment [Line Items]
Property and equipment, Useful Life	5 years
Property and equipment, gross	$ 194	186
Equipment [Member]
Property, Plant and Equipment [Line Items]
Property and equipment, Useful Life	5 years
Property and equipment, gross		71
Leasehold Improvements [Member]
Property, Plant and Equipment [Line Items]
Property and equipment, gross	$ 415	$ 406

Property and Equipment, net - A

Property and Equipment, net - Additional Information (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Property Plant And Equipment Capitalized Interest Costs [Abstract]
Depreciation expense	$ 212	$ 70	$ 16

Accrued Expenses - Schedule of

Accrued Expenses - Schedule of Accrued Expenses (Detail) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Payables and Accruals [Abstract]
Accrued payroll and related expenses	$ 2,008	$ 1,802
Accrued research and development expenses	892	3,727
Accrued restructuring	376
Accrued professional fees	347	422
Accrued other	110	161
Accrued expenses	$ 3,733	$ 6,112

Notes Payable - Additional Info

Notes Payable - Additional Information (Detail) - USD ($)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Debt Instrument [Line Items]
Line of credit facility description	Upon entering into the 2014 Credit Facility, the Company was obligated to make monthly, interest-only payments on any term loans funded under the 2014 Credit Facility until December 1, 2014 and, thereafter, to pay 36 consecutive, equal monthly installments of principal and interest from January 1, 2015 through December 1, 2017. As per the terms of the agreement, in June 2014, upon the completion of the Company’s IPO, the term of monthly, interest-only payments
Credit facility maturity date	Dec. 1, 2017
Line of credit facility annual interest rate	8.10%
Line of credit facility additional fee percentage	6.00%
Credit facility default amount	$ 300,000
Term Loan A [Member]
Debt Instrument [Line Items]
Charges to interest expense of debt outstanding	500,000
2014 Credit Facility [Member]
Debt Instrument [Line Items]
Covenants under credit facility	0
2014 Credit Facility [Member] | Secured Debt [Member]
Debt Instrument [Line Items]
Interest expense on credit facility	$ 500,000	$ 800,000	$ 900,000
Effective annual interest rate	10.80%
Credit Facility [Member]
Debt Instrument [Line Items]
Sale of voting equity threshold	50.00%

Notes Payable - Schedule of Not

Notes Payable - Schedule of Notes Payable (Detail) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Debt Instrument [Line Items]
Notes payable	$ 3,183	$ 6,119
Notes payable current portion	3,589	2,936
Notes payable, net of current portion		3,183
Notes payable, net of current portion		3,183
Notes payable, net of discount, long term		3,453
Secured Debt [Member] | Credit Facility [Member]
Debt Instrument [Line Items]
Debt discount, net of accretion	(9)	(36)
Accretion related to final payment	$ 415	$ 306

Notes Payable - Schedule of Est

Notes Payable - Schedule of Estimated Future Principal Payments (Detail) $ in Thousands	Dec. 31, 2016USD ($)
Debt Instruments [Abstract]
2,017	$ 3,183
Total	$ 3,183

Stockholders' Equity - Addition

Stockholders' Equity - Additional Information (Detail) - USD ($) $ / shares in Units, $ in Thousands	Jan. 28, 2015	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2016
Proceeds from offering, net of commissions and underwriting discounts		$ 130,044	$ 102,672
Payments of public offering costs		$ 473	$ 2,312
Preferred stock, shares authorized		5,000,000		5,000,000
Preferred stock, par value		$ 0.001		$ 0.001
Common stock, shares authorized		115,000,000		115,000,000
Common stock, par value		$ 0.001		$ 0.001
Follow-on Offering [Member]
Common stock issued	3,942,200
Common stock issued price per share	$ 35
Proceeds from offering, net of commissions and underwriting discounts	$ 130,000
Payments of public offering costs	$ 500

Stock-Based Awards - Additional

Stock-Based Awards - Additional Information (Detail) - USD ($)	Jan. 01, 2016	Dec. 31, 2014	Sep. 01, 2014	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014	Jun. 05, 2014
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock based compensation, stock options granted				1,527,559	992,505
Aggregate intrinsic value of stock options exercised				$ 100,000	$ 13,900,000
Proceeds from exercise of common stock options					$ 800,000
Weighted average grant-date fair value of stock options granted				$ 4.86	$ 28.97	$ 11.73
Unrecognized stock-based compensation cost				$ 14,100,000
Stock-based compensation recognized weighted average period				2 years 2 months 12 days
Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Proceeds from exercise of common stock options				$ 100,000
Employees [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock based compensation, stock options granted				1,519,559	988,505
Consultant [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock based compensation, stock options granted				8,000	4,000
Nonemployee Service Based Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of outstanding unvested shares held by nonemployees				6,401	9,363
Restricted Stock [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of restricted stock granted				0	0	0
Number of restricted stock units vested				0	0	0
Restricted Stock Units (RSUs) [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of restricted stock granted				13,273	4,769	0
Number of restricted stock units vested						0
Aggregate intrinsic value of restricted stock units vested during the period				$ 100,000	$ 100,000
Weighted average grant-date fair value of restricted stock units granted				$ 7.91	$ 34.46
Number of restricted stock units unvested		0		0	0	0
2006 Stock Option Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares of common stock authorized under stock option plan				1,889,150
Shares of common stock reserved for issuance				168,221
2006 Stock Option Plan [Member] | Minimum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options purchase price of common stock, percent of fair market value				100.00%
2006 Stock Option Plan [Member] | Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Maximum term of stock option				10 years
2014 Stock Option and Incentive Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares of common stock reserved for issuance				2,168,221
Percentage of outstanding shares of common stock				4.00%
Common stock available for issuance				2,107,295
Shares added to plan	1,089,700
2014 Employee Stock Purchase Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares of common stock reserved for issuance							265,000
Common stock available for issuance				219,797	257,460
Commencement date of first offering period			Sep. 1, 2014
End date of first offering period			Dec. 31, 2014
Commencement date of second offering period				Jan. 1, 2016	Jan. 1, 2015
End date of second offering period				Jun. 30, 2016	Jun. 30, 2015
Commencement date of third offering period				Jul. 1, 2016	Jul. 1, 2015
End date of third offering period				Dec. 31, 2016	Dec. 31, 2015
Stock-based awards, shares				37,663	7,540
2014 Employee Stock Purchase Plan [Member] | Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Discount from market price of the company's common stock offering		85.00%	85.00%

Stock-Based Awards - Assumption

Stock-Based Awards - Assumptions used to Determine Fair Value of Stock Options Granted (Detail)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Risk-free interest rate	1.40%	1.75%	1.90%
Expected term (in years)	6 years 2 months 5 days	6 years 3 months	6 years 3 months
Expected volatility	87.00%	87.00%	90.00%
Expected dividend yield	0.00%	0.00%	0.00%

Stock-Based Awards - Summary of

Stock-Based Awards - Summary of Stock Option Activity (Detail) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Shares issuable under options, beginning balance	2,555,110
Shares issuable under options, granted	1,527,559	992,505
Shares issuable under options, exercised	(35,000)
Shares issuable under options, forfeited	(932,666)
Shares issuable under options, ending balance	3,115,003	2,555,110
Shares issuable under options, options vested and expected to vest	3,080,777
Shares issuable under options, options exercisable	1,605,537
Weighted-average exercise price, beginning balance	$ 19.76
Weighted-average exercise price, granted	6.65
Weighted-average exercise price, exercised	0.75
Weighted-average exercise price, forfeited	16.90
Weighted-average exercise price, ending balance	14.40	$ 19.76
Weighted-average exercise price, options vested and expected to vest	14.40
Weighted-average exercise price, options exercisable	$ 14.18
Average remaining contractual life	7 years 2 months 12 days
Average remaining contractual life, options vested and expected to vest	7 years 2 months 12 days
Average remaining contractual life, options exercisable	5 years 6 months
Aggregate intrinsic value	$ 1,038
Aggregate intrinsic value, options vested and expected to vest	1,038
Aggregate intrinsic value, options exercisable	$ 1,036

Stock-Based Awards - Summary 48

Stock-Based Awards - Summary of Stock-Based Compensation Expense Related to Stock Options and Restricted Common Stock (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	$ 9,933	$ 8,582	$ 1,553
Research and Development [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	3,543	2,930	490
General and Administrative [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total stock-based compensation expense	$ 6,390	$ 5,652	$ 1,063

Net Loss Per Share - Computatio

Net Loss Per Share - Computation of Basic and Diluted Earnings Per Share (Detail) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Numerator:
Net loss									$ (57,878)	$ (74,286)	$ (36,478)
Accretion of redeemable convertible preferred stock to redemption value											(92)
Net loss attributable to common stockholders	$ (10,439)	$ (14,675)	$ (15,028)	$ (17,736)	$ (23,174)	$ (19,884)	$ (17,756)	$ (13,472)	$ (57,878)	$ (74,286)	$ (36,570)
Denominator:
Weighted average common shares outstanding, basic and diluted	27,332,515	27,322,907	27,272,225	27,263,435	27,238,079	27,138,667	27,011,960	25,615,282	27,297,934	26,756,079	12,189,155
Net loss per share attributable to common stockholders, basic and diluted	$ (0.38)	$ (0.54)	$ (0.55)	$ (0.65)	$ (0.85)	$ (0.73)	$ (0.66)	$ (0.53)	$ (2.12)	$ (2.78)	$ (3)

Net Loss Per Share - Summary of

Net Loss Per Share - Summary of Common Stock Equivalents Outstanding (Detail) - shares	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Options to Purchase Common Stock [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Securities excluded from computation of earnings per share	3,115,003	2,555,110	2,008,574

Commitments and Contingencies -

Commitments and Contingencies - Additional Information (Detail)	Jan. 01, 2017ft²	Oct. 01, 2015	Jan. 31, 2017	Mar. 31, 2015Option	Dec. 31, 2017USD ($)	Dec. 31, 2016USD ($)	Dec. 31, 2015USD ($)	Dec. 31, 2014USD ($)
Other Commitments [Line Items]
Operating lease, rental expense						$ 400,000	$ 300,000	$ 200,000
Issuance of common stock in lieu of milestone payment								3,569,000
Development Based Milestones [Member]
Other Commitments [Line Items]
Milestone payments due						0	$ 0	7,000,000
Issuance of common stock in lieu of milestone payment								$ 3,600,000
Subsequent Licensed Product [Member]
Other Commitments [Line Items]
Licensing fees per product maximum						$ 1,300,000
Boston Office Space [Member]
Other Commitments [Line Items]
Lease expiration date						Jul. 31, 2017
Lease extension period						3 years
Boston Office Space [Member] | Scenario, Forecast [Member]
Other Commitments [Line Items]
Sublease rental income					$ 100,000
Additional Boston Office Space [Member]
Other Commitments [Line Items]
Lease expiration date				Jul. 31, 2017
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
Maximum [Member] | Product Commercialization Milestones [Member]
Other Commitments [Line Items]
Milestone payments						$ 12,500,000
Subsequent Event [Member] | Boston Office Space [Member]
Other Commitments [Line Items]
Lease expiration date	Dec. 31, 2017		Jul. 31, 2020
Subleased area | ft²	2,976

Commitments and Contingencies52

Commitments and Contingencies - Schedule of Future Minimum Lease Payments for Operating Leases (Detail) $ in Thousands	Dec. 31, 2016USD ($)
Commitments and Contingencies Disclosure [Abstract]
2,017	$ 300
2,018	106
2,019	82
Total	$ 488

Commitments and Contingencies53

Commitments and Contingencies - Research and Development Expenses Related to License Agreements (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Commitments And Contingencies [Line Items]
License, milestone, and license maintenance fees	$ 39,936	$ 54,618	$ 27,391
Intellectual Property Licenses [Member]
Commitments And Contingencies [Line Items]
License, milestone, and license maintenance fees			7,019
Intellectual Property Licenses [Member] | License Agreements [Member]
Commitments And Contingencies [Line Items]
License, milestone, and license maintenance fees			$ 7,019

Income Taxes - Additional Infor

Income Taxes - Additional Information (Detail) - USD ($)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Income Taxes Disclosure [Line Items]
Income tax benefit	$ 0	$ 0	$ 0
Operating loss carryforwards, federal	13,100,000
Operating loss carryforwards, state	1,900,000
Uncertain tax position	0
Gross deferred tax assets	97,720,000	74,541,000
Capitalized research and development expenses	59,489,000	46,568,000
Unrecognized tax benefits	0	$ 0
Accounting Standards Update 2006 [Member]
Income Taxes Disclosure [Line Items]
Operating loss carryforwards, federal	9,400,000
Operating loss carryforwards, state	7,200,000
Capitalized research and development expenses	3,400,000
Net operating loss carryforwards tax effected, Federal	3,200,000
Net operating loss carryforwards tax effected, State	400,000
Capitalized research and development expenses tax effected	1,300,000
Accounting Standards Update 2016-09 [Member]
Income Taxes Disclosure [Line Items]
Operating loss carryforwards, federal	9,400,000
Operating loss carryforwards, state	7,200,000
Capitalized research and development expenses	3,400,000
Net operating loss carryforwards tax effected, Federal	3,200,000
Net operating loss carryforwards tax effected, State	400,000
Capitalized research and development expenses tax effected	1,300,000
Stock Option [Member]
Income Taxes Disclosure [Line Items]
Operating loss carryforwards, federal	9,400,000
Operating loss carryforwards, state	7,200,000
Gross deferred tax assets	12,800,000
Capitalized research and development expenses	3,400,000
Domestic Tax Authority [Member]
Income Taxes Disclosure [Line Items]
Net operating loss carryforwards	$ 49,100,000
Net operating loss carryforwards, beginning of expiration period	2,026
Research and development tax credit carryforwards, beginning of expiration period	2,026
State and Local Jurisdiction [Member]
Income Taxes Disclosure [Line Items]
Net operating loss carryforwards	$ 35,900,000
Net operating loss carryforwards, beginning of expiration period	2,030
Research and development tax credit carryforwards, beginning of expiration period	2,021

Income Taxes - Schedule of Dome

Income Taxes - Schedule of Domestic and Foreign Components of Loss Before Income Taxes (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Income Tax Disclosure [Abstract]
Domestic	$ (57,799)	$ (72,147)	$ (35,818)
Foreign	(79)	(2,139)	(660)
Loss before income taxes	$ (57,878)	$ (74,286)	$ (36,478)

Income Taxes - Reconciliation o

Income Taxes - Reconciliation of Federal Statutory Income Tax Rate (Detail)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Income Tax Disclosure [Abstract]
Federal statutory income tax rate	(34.00%)	(34.00%)	(34.00%)
Federal and state research and development tax credit	(2.90%)	(3.90%)	(1.90%)
State taxes, net of federal benefit	(3.90%)	(3.90%)	(4.00%)
Orphan drug tax credit	(1.30%)	(3.50%)	(3.20%)
Stock compensation expense	0.70%	0.90%	0.60%
Nondeductible Australia research and development expenses	0.00%	1.00%	0.60%
Other items	1.30%	0.10%	2.40%
Change in deferred tax asset valuation allowance	40.10%	43.30%	39.50%
Effective income tax rate	0.00%	0.00%	0.00%

Income Taxes - Schedule of Net

Income Taxes - Schedule of Net Deferred Tax Assets (Detail) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Noncurrent deferred tax assets:
Capitalized research and development expenses	$ 59,489	$ 46,568
Net operating loss carryforwards	14,991	11,186
Tax credit carryforwards	14,297	11,570
Capitalized legal expenses	2,119	1,773
Stock-based compensation	6,027	2,780
Accrued expenses	783	648
Other temporary differences	14	16
Total noncurrent deferred tax assets	97,720	74,541
Total gross deferred tax assets	97,720	74,541
Valuation allowance	(97,720)	(74,541)	$ (42,398)	$ (27,831)
Net deferred tax assets	$ 0	$ 0

Income Taxes - Summary of Chang

Income Taxes - Summary of Changes in the Valuation Allowance for Deferred Tax Assets (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Income Tax Disclosure [Abstract]
Valuation allowance as of beginning of year	$ 74,541	$ 42,398	$ 27,831
Decreases recorded as benefit to income tax provision	0	0	0
Increases recorded to income tax provision	23,179	32,143	14,567
Valuation allowance as of end of year	$ 97,720	$ 74,541	$ 42,398

Retirement Plan - Additional In

Retirement Plan - Additional Information (Detail) - USD ($)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Defined Contribution Plan Disclosure [Line Items]
Percentage of employer's contribution on employee's base salary	2.00%
Contribution expense	$ 200,000	$ 100,000
Maximum [Member]
Defined Contribution Plan Disclosure [Line Items]
Contribution expense			$ 100,000

Australia Research and Develo60

Australia Research and Development Tax Incentive - Additional Information (Detail) - USD ($)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Research and Development Tax Incentive [Line Items]
Unrealized foreign currency transaction gains (losses)	$ (6,000)	$ (82,000)	$ (93,000)
Australia [Member]
Research and Development Tax Incentive [Line Items]
Tax incentive receivable	300,000	1,300,000
Maximum [Member] | Zafgen Australia Pty Limited [Member]
Research and Development Tax Incentive [Line Items]
Unrealized foreign currency transaction gains (losses)	$ (100,000)	(100,000)	(100,000)
Research and Development [Member]
Research and Development Tax Incentive [Line Items]
Percentage of refundable tax incentive	45.00%
Reduction to research and development expenses	$ 300,000	$ 1,400,000	$ 400,000
Research and Development [Member] | Australia [Member]
Research and Development Tax Incentive [Line Items]
Percentage of reduction in research and development costs	45.00%

Restructuring - Additional Info

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

Restructuring - Summary of Rest

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

Restructuring - Summary of Re63

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

Quarterly Financial Data - Sche

Quarterly Financial Data - Schedule of Unaudited Consolidated Financial Statements (Detail) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Quarterly Financial Information Disclosure [Abstract]
Revenue	$ 0	$ 0	$ 0	$ 0	$ 0	$ 0	$ 0	$ 0	$ 0	$ 0	$ 0
Operating expenses	10,475	14,831	15,062	17,857	23,246	19,717	17,610	13,240	58,225	73,813	35,532
Net loss	$ (10,439)	$ (14,675)	$ (15,028)	$ (17,736)	$ (23,174)	$ (19,884)	$ (17,756)	$ (13,472)	$ (57,878)	$ (74,286)	$ (36,570)
Net loss per share, basic and diluted	$ (0.38)	$ (0.54)	$ (0.55)	$ (0.65)	$ (0.85)	$ (0.73)	$ (0.66)	$ (0.53)	$ (2.12)	$ (2.78)	$ (3)
Weighted average common shares outstanding, basic and diluted	27,332,515	27,322,907	27,272,225	27,263,435	27,238,079	27,138,667	27,011,960	25,615,282	27,297,934	26,756,079	12,189,155