aTyr Pharma (ATYR) 10-Q 12 May 20 2020 Q1 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	3 Months Ended
	Mar. 31, 2020	May 08, 2020
Cover [Abstract]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Mar. 31, 2020
Document Fiscal Year Focus	2020
Document Fiscal Period Focus	Q1
Document Quarterly Report	true
Document Transition Report	false
Security Exchange Name	NASDAQ
Trading Symbol	LIFE
Entity Registrant Name	aTYR PHARMA INC
Entity Central Index Key	0001339970
Entity Current Reporting Status	Yes
Entity Interactive Data Current	Yes
Current Fiscal Year End Date	--12-31
Entity Filer Category	Non-accelerated Filer
Entity Shell Company	false
Entity Small Business	true
Entity Emerging Growth Company	true
Entity Ex Transition Period	true
Entity Common Stock, Shares Outstanding		9,352,498
Entity File Number	001-37378
Entity Tax Identification Number	20-3435077
Entity Address, Address Line One	3545 John Hopkins Court
Entity Address, Address Line Two	Suite #250
Entity Address, City or Town	San Diego
Entity Address, State or Province	CA
Entity Incorporation, State or Country Code	DE
Entity Address, Postal Zip Code	92121
City Area Code	(858)
Local Phone Number	731-8389
Title of 12(b) Security	Common Stock, par value $0.001 per share

Condensed Consolidated Balance

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Mar. 31, 2020	Dec. 31, 2019
Current assets:
Cash and cash equivalents	$ 39,453	$ 9,210
Available-for-sale investments	10,376	21,934
Prepaid expenses and other assets	545	781
Total current assets	50,374	31,925
Property and equipment, net	1,281	1,270
Right-of-use assets	2,643	2,821
Other assets	149	172
Total assets	54,447	36,188
Current liabilities:
Accounts payable	748	847
Accrued expenses	1,908	2,376
Contract liability	143	208
Current portion of operating lease liability	780	755
Current portion of long-term debt, net of issuance costs and discount	6,866	8,737
Total current liabilities	10,445	12,923
Long-term operating lease liability, net of current portion	2,035	2,239
Commitments and contingencies (Note 4)
Stockholders’ equity:
Preferred stock, $0.001 par value per share; 5,000,000 undesignated authorized shares; Class X Convertible Preferred Stock issued and outstanding shares – 0 and 1,643,961 as of March 31, 2020 (unaudited) and December 31, 2019, respectively		2
Common stock, $0.001 par value per share; 10,714,286 authorized shares; issued and outstanding shares – 9,352,498 and 3,891,787 as of March 31, 2020 (unaudited) and December 31, 2019, respectively	9	4
Additional paid-in capital	362,723	343,524
Accumulated other comprehensive loss	(53)	(40)
Accumulated deficit	(320,551)	(322,304)
Total aTyr Pharma stockholders’ equity	42,128	21,186
Noncontrolling interest in Pangu BioPharma Limited	(161)	(160)
Total stockholders' equity	41,967	21,026
Total liabilities and stockholders’ equity	$ 54,447	$ 36,188

Condensed Consolidated Balanc_2

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Mar. 31, 2020	Dec. 31, 2019
Preferred stock, par value	$ 0.001	$ 0.001
Preferred stock, shares authorized	5,000,000	5,000,000
Common stock, par value	$ 0.001	$ 0.001
Common stock, shares authorized	10,714,286	10,714,286
Common stock, shares issued	9,352,498	3,891,787
Common stock, shares outstanding	9,352,498	3,891,787
Class X Convertible Preferred Stock [Member]
Preferred stock, shares issued	0	1,643,961
Preferred stock, shares outstanding	0	1,643,961

Condensed Consolidated Statemen

Condensed Consolidated Statements of Operations (Unaudited) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
Revenues:
Total revenues	$ 8,065
Operating expenses:
Research and development	3,616	$ 3,345
General and administrative	2,590	2,532
Total operating expenses	6,206	5,877
Income (loss) from operations	1,859	(5,877)
Total other expense, net	(107)	(260)
Consolidated net income (loss)	1,752	(6,137)
Net loss attributable to noncontrolling interest in Pangu BioPharma Limited	1
Net income (loss) attributable to aTyr Pharma, Inc.	$ 1,753	$ (6,137)
Basic net income (loss) per share	$ 0.25	$ (2.54)
Shares used in computing basic net income (loss) per share	6,881,791	2,418,674
Diluted net income (loss) per share	$ 0.25	$ (2.54)
Shares used in computing diluted net income (loss) per share	6,884,797	2,418,674
License Revenues [Member]
Revenues:
Total revenues	$ 8,065

Condensed Consolidated Statem_2

Condensed Consolidated Statements of Comprehensive Income (Loss) (Unaudited) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
Statement Of Income And Comprehensive Income [Abstract]
Consolidated net income (loss)	$ 1,752	$ (6,137)
Other comprehensive gain (loss):
Change in unrealized gain (loss) on available-for-sale investments, net of tax	(13)	20
Comprehensive income (loss)	1,739	(6,117)
Comprehensive loss attributable to noncontrolling interest Pangu BioPharma Limited	1
Comprehensive income (loss) attributable to aTyr Pharma, Inc. common stockholders	$ 1,740	$ (6,117)

Condensed Consolidated Statem_3

Condensed Consolidated Statements of Stockholders' Equity (Unaudited) - USD ($) shares in Thousands, $ in Thousands	Total	Common Stock [Member]	Additional Paid-In Capital [Member]	Other Comprehensive Gain/(Loss) [Member]	Accumulated Deficit [Member]	Noncontrolling Interest [Member]	Convertible Preferred Stock [Member]
Begining balance, Shares at Dec. 31, 2018		2,186,389					2,285,952
Conversion of preferred stock to common stock, shares		229,283					(641,991)
Issuance of common stock from at the market offerings, net of offering costs	$ 1,381		$ 1,381
Issuance of common stock from at the market offerings, net of offering costs, Shares		193,670
Stock-based compensation	571		571
Net unrealized gain (loss) on investments, net of tax	20			$ 20
Consolidated net income (loss)	(6,137)
Ending balance, Shares at Mar. 31, 2019		2,609,342					1,643,961
Beginning balance at Dec. 31, 2018	33,650	$ 2	332,407	(60)	$ (298,701)		$ 2
Net income (loss)	(6,137)				(6,137)
Ending balance at Mar. 31, 2019	29,485	2	334,359	(40)	(304,838)		2
Beginning balance at Dec. 31, 2019	21,026	$ 4	343,524	(40)	(322,304)	$ (160)	$ 2
Begining balance, Shares at Dec. 31, 2019		3,891,787					1,643,961
Conversion of preferred stock to common stock		$ 1	1				$ (2)
Conversion of preferred stock to common stock, shares		587,444					(1,643,961)
Issuance of common stock upon release of restricted stock units, Shares		2,679
Issuance of common stock from underwritten follow-on offering, net of offering costs	18,779	$ 4	18,775
Issuance of common stock from underwritten follow-on offering, net of offering costs, shares		4,870,588
Stock-based compensation	423		423
Net unrealized gain (loss) on investments, net of tax	(13)			(13)
Consolidated net income (loss)	1,752				1,753	(1)
Ending balance at Mar. 31, 2020	41,967	$ 9	$ 362,723	$ (53)	$ (320,551)	$ (161)
Ending balance, Shares at Mar. 31, 2020		9,352,498
Beginning balance at Dec. 31, 2019	21,186
Net income (loss)	1,753
Ending balance at Mar. 31, 2020	$ 42,128

Condensed Consolidated Statem_4

Condensed Consolidated Statements of Cash Flows (Unaudited) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
Cash flows from operating activities:
Consolidated net income (loss)	$ 1,752	$ (6,137)
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities:
Depreciation and amortization	157	167
Stock-based compensation	423	571
Debt discount accretion and non-cash interest expense	129	201
Accretion of discount of available-for-sale investment securities	(24)	(106)
Amortization of right-of-use assets	201	169
Loss on disposal of property and equipment	6
Changes in operating assets and liabilities
Collaboration receivable		(630)
Prepaid expenses and other assets	236	97
Accounts payable and accrued expenses	(578)	(985)
Contract liability	(65)	630
Operating lease liability	(179)
Net cash provided by (used in) operating activities	2,058	(6,023)
Cash flows from investing activities:
Purchases of property and equipment	(166)	(10)
Purchases of available-for-sale investment securities	(3,081)	(13,995)
Maturities of available-for-sale investment securities	14,650	10,650
Proceeds from sale of property and equipment	3
Net cash provided by (used in) investing activities	11,406	(3,355)
Cash flows from financing activities:
Proceeds from issuance of common stock through at the market offerings, net of offering costs		1,381
Proceeds from issuance of common stock through underwritten follow-on offering, net of offering costs	18,779
Repayments on borrowings	(2,000)	(2,000)
Net cash provided by (used in) financing activities	16,779	(619)
Net change in cash and cash equivalents	30,243	(9,997)
Cash and cash equivalents at beginning of period	9,210	22,962
Cash and cash equivalents at the end of period	$ 39,453	$ 12,965

Organization, Business, Basis o

Organization, Business, Basis of Presentation and Summary of Significant Accounting Policies	3 Months Ended
	Mar. 31, 2020
Accounting Policies [Abstract]
Organization, Business, Basis of Presentation and Summary of Significant Accounting Policies	1. Organization, Business, Basis of Presentation and Summary of Significant Accounting Policies Organization and Business aTyr Pharma, Inc. (we, us, and our) was incorporated in the state of Delaware on September 8, 2005. We are focused on the discovery and development of innovative medicines based on novel immunological pathways. Principles of Consolidation Our condensed consolidated financial statements include our accounts and our 98% majority-owned subsidiary in Hong Kong, Pangu BioPharma Limited (Pangu BioPharma). All intercompany transactions and balances are eliminated in consolidation. Unaudited Interim Financial Information The accompanying interim condensed consolidated financial statements are unaudited. These unaudited interim financial statements have been prepared in accordance with United States generally accepted accounting principles (GAAP) and follow the requirements of the United States Securities and Exchange Commission (SEC) for interim reporting. As permitted under those rules, certain footnotes or other financial information that are normally required by GAAP can be condensed or omitted. In our opinion, the unaudited interim financial statements have been prepared on the same basis as the audited financial statements and include all adjustments, which include only normal recurring adjustments, necessary for the fair presentation of our financial position and our results of operations and cash flows for periods presented. These statements do not include all disclosures required by GAAP and should be read in conjunction with our financial statements and accompanying notes for the fiscal year ended December 31, 2019, contained in our Annual Report on Form 10-K filed with the SEC on March 26, 2020. The results of the interim periods are not necessarily indicative of the results expected for the full fiscal year or any other interim period or any future year or period. Reverse Stock Split On June 28, 2019, we filed a Certificate of Amendment to our Restated Certificate of Incorporation with the Secretary of State of the Risks and Uncertainties In December 2019, COVID-19, a novel strain of coronavirus, was first reported in Wuhan, China, has been declared a pandemic by the World Health Organization and has spread to over 100 countries, including the United States. The impact of this pandemic has been and will likely continue to be extensive in many aspects of society, which has resulted in and will continue to cause significant disruptions to the global economy, as well as businesses and capital markets around the world. Impacts to our business have included the delay in enrollment of our Phase 1b/2a clinical trial in patients with pulmonary sarcoidosis and the discontinuation of some patients in that trial, temporary closures of portions of our facilities and those of our licensees and collaborators, disruptions or restrictions on our employee's ability to travel and delays in certain research and development activities. Other potential impacts to our business include, but are not limited to disruptions to or delays in other clinical trials, third-party manufacturing supply and other operations, the potential diversion of healthcare resources away from the conduct of clinical trials to focus on pandemic concerns, interruptions or delays in the operations of the U.S. Food and Drug Administration or other regulatory authorities, and our ability to raise capital and conduct business development activities. . Liquidity and Financial Condition We have incurred losses and negative cash flows from operations since our inception. As of March 31, 2020, we had an accumulated deficit of $320.6 million and we expect to continue to incur net losses for the foreseeable future. We believe that our existing cash, cash equivalents and available-for-sale investments of $49.8 million as of March 31, 2020 will be sufficient to meet our anticipated cash requirements for a period of at least one year from the filing date of this Quarterly Report on Form 10-Q. We do not expect to generate any revenues from product sales unless and until we successfully complete development and obtain regulatory approval for one or more of our product candidates, which we expect will take a number of years at a minimum. If we obtain regulatory approval for any of our product candidates, we expect to incur significant commercialization expenses related to product sales, marketing, manufacturing and distribution. Accordingly, we will need to raise substantial additional capital to fund our operations. The amount and timing of our future funding requirements will depend on many factors, including, but not limited to, the pace and results of our preclinical and clinical development efforts and the timing and nature of the regulatory approval process for our product candidates. We anticipate that we will seek to fund our operations through equity offerings, grant funding, collaborations, strategic partnerships and/or licensing arrangements, and when we are closer to commercialization of our product candidates potentially through debt financings. However, we may be unable to raise additional capital or enter into such arrangements when needed on favorable terms or at all. As a result of the COVID-19 pandemic and actions taken to slow its spread, the global credit and financial markets have recently experienced extreme volatility and disruptions, including diminished liquidity and credit availability, declines in consumer confidence, declines in economic growth, increases in unemployment rates and uncertainty about economic stability. If the equity and credit markets continue to deteriorate, it may make any additional debt or equity financing more difficult, more costly and more dilutive. Our failure to raise capital or enter into applicable arrangements when needed would have a negative impact on our financial condition and ability to develop our product candidates. Use of Estimates Our condensed consolidated financial statements are prepared in accordance with GAAP. The preparation of our condensed consolidated financial statements requires us to make estimates and assumptions that impact the reported amounts of assets, liabilities and expenses and the disclosure of contingent assets and liabilities in our condensed consolidated financial statements and accompanying notes. The most significant estimates in our condensed consolidated financial statements relate to the clinical trials and research and development expenses. Although these estimates are based on our knowledge of current events and actions we may undertake in the future, actual results may ultimately differ materially from these estimates and assumptions. Though the impact of the COVID-19 pandemic to our business and operating results presents additional uncertainty, we continue to use the best information available to us in our critical accounting estimates. Leases We follow Accounting Standards Codification (ASC) Topic 842, Leases We elected the package of practical expedients permitted under the transition guidance within the new standard, which among other things, allowed us to exclude from our condensed consolidated balance sheets recognition of leases having a term of 12 months or less (short-term leases) and we elected to not separate lease components and non-lease components for our long-term leases. Rent expense for the operating lease is recognized on a straight-line basis over the lease term and is included in operating expenses in our condensed consolidated statements of operations. Revenue Recognition We evaluate our agreements under ASC Topic 606, Revenue from Contracts with Customers and ASC Topic 808, Collaborative Arrangements . . In determining the appropriate amount of revenue to be recognized as we fulfill our obligations under our agreement, we perform the following steps: (i) identification of the promised goods or services in the contract; (ii) determination of whether the promised goods or services are performance obligations including whether they are distinct in the context of the contract; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations; and (v) recognition of revenue when (or as) we satisfy each performance obligation. As part of the accounting for these arrangements, we must develop assumptions that require judgment to determine the stand-alone selling price for each performance obligation identified in the contract. We use key assumptions to determine the stand-alone selling price, which may include forecasted revenues, development timelines, reimbursement rates for personnel costs, discount rates and probabilities of technical and regulatory success. We recognize revenue in one of two ways, over time or at a point in time. We recognize revenue over time when we are executing on our performance obligation over time and our partner receives benefit over time. For example, we recognize revenue over time when we provide research and development services. We recognize revenue at a point in time when we transfer control of a distinct performance obligation to our partner. For example, if Basic and Diluted Basic Net Income (Loss) Per Share Basic net income (loss) per share is calculated by dividing the net income (loss) by the weighted average number of common shares outstanding for the period, without consideration for common stock equivalents and adjusted for the weighted average number of common shares outstanding that are subject to repurchase. Diluted Net Income (Loss) Per Share For the three months ended March 31, 2020, we had net income available to common stockholders. As a result, we computed diluted net income per share using the weighted average number of common shares and dilutive common equivalent shares outstanding during the period. Dilutive common equivalent shares outstanding included 3,006 shares of restricted stock units. For the three months ended March 31, 2020, the calculation excluded the following common equivalent shares because the effect on diluted earnings per share was anti-dilutive: Common stock warrants 13,904 Common stock options and restricted stock units 486,142 Employee stock purchase plan 1,958 502,004 For the three months ended March 31, 2019, common stock from the following would have had an anti-dilutive effect on net loss per share (in common share equivalents): Class X Preferred Stock (if-converted to common stock) 587,445 Common stock warrants 477,639 Common stock options and restricted stock units 404,977 Employee stock purchase plan 1,610 1,471,671 Recent Accounting Pronouncements In June 2016, the Financial Accounting Standards Board (FASB) issued Accounting Standards Update (ASU) No. 2016-13, Financial Instruments – Credit Losses to provide financial statement users with more decision-useful information about the expected credit losses on financial instruments and other commitments to extend credit held by a reporting entity at each reporting date. To achieve this objective, the amendments in Topic 326 replace the incurred loss impairment methodology in current GAAP with a methodology that reflects expected credit losses and requires consideration of a broader range of reasonable and supportable information to inform credit loss estimates. Topic 326 are effective for fiscal years beginning after December 15, 2022, including interim periods within those fiscal years for small reporting companies. We are currently evaluating the impact of Topic 326 and do not expect the adoption of this guidance will have a material impact on our condensed consolidated financial position or results of operations. In December 2019, the FASB issued ASU No. 2019-12, Income Taxes Simplifying the Accounting for Income Taxes

Fair Value Measurements

Fair Value Measurements	3 Months Ended
	Mar. 31, 2020
Fair Value Disclosures [Abstract]
Fair Value Measurements	2. Fair Value Measurements The carrying amounts of cash equivalents, prepaid and other assets, accounts payable and accrued liabilities are considered to be representative of their respective fair values because of the short-term nature of those instruments. Based on the borrowing rates currently available to us for loans with similar terms, which is considered a Level 2 input, we believe that the carrying value of our long-term debt approximates their fair value. Investment securities are recorded at fair value. The accounting guidance defines fair value, establishes a consistent framework for measuring fair value and expands disclosure for each major asset and liability category measured at fair value on either a recurring or nonrecurring basis. Fair value is defined as an exit price, representing the amount that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants. As such, fair value is a market-based measurement that should be determined based on assumptions that market participants would use in pricing an asset or liability. As a basis for considering such assumptions, the accounting guidance establishes a three-tier fair value hierarchy, which prioritizes the inputs used in measuring fair value as follows: Level 1: Observable inputs such as quoted prices in active markets. Level 2: Inputs, other than the quoted prices in active markets that are observable either directly or indirectly. Level 3: Unobservable inputs in which there is little or no market data, which require the reporting entity to develop its own assumptions. Financial assets measured at fair value on a recurring basis consist of investment securities. Investment securities are recorded at fair value, defined as the exit price in the principal market in which we would transact, representing the amount that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants. Level 2 securities are valued using quoted market prices for similar instruments, non-binding market prices that are corroborated by observable market data, or discounted cash flow techniques and include our investments in corporate debt securities and commercial paper. We have no financial liabilities measured at fair value on a recurring basis. None of our non-financial assets and liabilities is recorded at fair value on a non-recurring basis. No transfers between levels have occurred during the periods presented. Assets measured at fair value on a recurring basis are as follows (in thousands): Fair Value Measurements Using Total Quoted Active for Assets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) As of March 31, 2020 Assets: Current: Cash equivalents $ 34,674 $ 34,674 $ — $ — Available-for-sale investments, short-term: Asset-backed securities 3,100 — 3,100 — Commercial paper 5,076 — 5,076 — Corporate debt securities 2,200 — 2,200 — Total short-term investments 10,376 — 10,376 — Total assets measured at fair value $ 45,050 $ 34,674 $ 10,376 $ — Fair Value Measurements Using Total Quoted Active for Assets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) As of December 31, 2019 Assets: Current: Cash equivalents $ 8,248 $ 8,248 $ — $ — Available-for-sale investments, short-term: Asset-backed securities 6,304 — 6,304 — Commercial paper 7,568 — 7,568 — Corporate debt securities 8,062 — 8,062 — Total short-term investments 21,934 — 21,934 — Total assets measured at fair value $ 30,182 $ 8,248 $ 21,934 $ — As of March 31, 2020 and December 31, 2019, available-for-sale investments are detailed as follows (in thousands): March 31, 2020 Gross Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Market Value Available-for-sale investments, short-term: Asset-backed securities $ 3,102 $ — $ (2 ) $ 3,100 Commercial paper 5,077 — — 5,077 Corporate debt securities 2,200 — (1 ) 2,199 $ 10,379 $ — $ (3 ) $ 10,376 December 31, 2019 Gross Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Market Value Available-for-sale investments, short-term: Asset-backed securities $ 6,299 $ 5 $ — $ 6,304 Commercial paper 7,568 — — 7,568 Corporate debt securities 8,057 5 — 8,062 $ 21,924 $ 10 $ — $ 21,934 As of March 31, 2020, all of our available-for-sale investments had a variety of effective maturity dates of less than one year. As of March 31, 2020, four out of ten of the available-for-sale investments were in gross unrealized loss positions. At each reporting date, we perform an evaluation of impairment to determine if any unrealized losses are other-than-temporary. Factors considered in determining whether a loss is other-than-temporary include the length of time and extent to which fair value has been less than the cost basis, the financial condition of the issuer, and our intent and ability to hold the investment until recovery of its amortized cost basis. We intend, and have the ability, to hold our investments in unrealized loss positions until their amortized cost basis has been recovered.

License and Other Agreements

License and Other Agreements	3 Months Ended
	Mar. 31, 2020
License Agreements [Abstract]
License and Other Agreements	3. License and Other Agreements CSL Behring In March 2019, we entered into a research collaboration and option agreement with CSL Behring (CSL) for the development of product candidates derived from up to four tRNA synthetases from our preclinical pipeline (CSL Agreement). Under the terms of the CSL Agreement, CSL will fund all research and development activities related to the development of the applicable product candidates for the duration of the collaboration. CSL reimburses us for all research and development activities. The research and development activities will be performed in six phases by both parties. The first phase totaling $0.6 million was funded in May 2019 and future phases will be funded on a quarterly basis. In addition, CSL will pay a total of up to $4.25 million per synthetase program ($17.0 million if all four synthetase programs advance) in option fees based on achievement of research milestones and CSL’s determination to continue development. As of March 31, 2020, no research milestone has been met. Moreover, aTyr will grant CSL an option to negotiate licenses for worldwide rights to each investigational new drug (IND) candidate that emerges from this research collaboration. Specific license terms will be negotiated during an exclusivity period following the exercise of each program option. CSL has the right to terminate the CSL Agreement in its entirety or with respect to one or more synthetases upon 45 days notice. Either party has the right to terminate the agreement upon material breach of obligation or insolvency. We assessed our research collaboration with CSL in accordance with Topic 606 and concluded that CSL is a customer. We identified the following performance obligations under the CSL Agreement: 1) research services; and 2) participation in the Joint Steering Committee. We concluded that the performance obligations are interrelated and do not have a standalone basis. CSL has the right to terminate the research collaboration upon 45 days notice, which is considered to be the legally enforceable contract term. Therefore, during the first phase of research services, we have a 45 day performance obligation and all research services beyond the initial 45 days performance obligation are considered a material right. In addition, each phase of research services represents a separate customer option since CSL must provide written notice of its intent to advance to the next phase. Under the CSL Agreement, CSL is obligated to pay us for the costs incurred by us under the research programs. The payment of $0.6 million for the first phase of the research program received in May 2019 was considered fixed consideration and we will recognize revenue on the payment for the research service performance obligation as the services are performed. We are utilizing a cost-based input method to measure proportional performance and to calculate the corresponding amount of revenue to recognize. We believe this is the best measure of progress because other measures do not reflect how we transfer the performance obligation to our counterparty. In applying the cost-based input methods of revenue recognition, we use actual costs incurred relative to budgeted costs to fulfill the combined performance obligation. These costs consist primarily of third-party contract costs and internal full-time equivalent effort. A cost-based input method of revenue recognition requires us to make estimates of costs to complete the performance obligations. The cumulative effect of revisions to estimated costs to complete the performance obligations will be recorded in the period in which changes are identified and amounts can be reasonably estimated. A significant change in these assumptions and estimates could have a material impact on the timing and amount of revenue recognized in future periods. The option fees based on research milestones under the CSL Agreement are variable consideration. Because they are binary in nature, we will use the “most-likely” method to evaluate whether the milestones should be included. However, the milestones are only payable upon CSL’s decision to proceed to the next research phase for any program, and are therefore subject to CSL’s sole discretion. Accordingly, the milestones are fully constrained and we will not recognize revenue related to these amounts until we have received notification from CSL that they would like to proceed with the next phase of a research program. For the three months ended March 31, 2020, we recognized $0.2 million as license revenue under the CSL Agreement. Kyorin Pharmaceutical Co., Ltd. In January 2020, we entered into a license agreement with Kyorin Pharmaceutical Co., Ltd. (Kyorin) for the development and commercialization of ATYR1923 for interstitial lung diseases (ILDs) in Japan. Under the collaboration and license agreement with Kyorin (Kyorin Agreement), Kyorin received an exclusive right to develop and commercialize ATYR1923 in Japan for all forms of ILDs. We received an $8.0 million upfront payment and we are eligible to receive an additional $167.0 million in the aggregate upon achievement of certain development, regulatory and sales milestones, as well as tiered royalties ranging from the mid-single digits to mid-teens on net sales in Japan. Under the terms of the Kyorin Agreement, Kyorin will fund all research, development, regulatory, marketing and commercialization activities in Japan. Following the first anniversary of the effective date of the Kyorin Agreement, Kyorin has the right to terminate the agreement for any reason upon 90 days advance written notice. Either party may terminate the Kyorin Agreement in the event that the other party breaches the agreement and fails to cure the breach, becomes insolvent or challenges certain of the intellectual property rights licensed under the agreement . We assessed our research collaboration with Kyorin in accordance with Topic 606 and concluded that Kyorin is a customer. We identified the following performance obligations under the Kyorin Agreement: 1) the license of ATYR1923 for ILDs in Japan; and 2) free clinical trial material for Kyorin’s Phase 1 clinical trial. The $8.0 million upfront payment received from Kyorin is non-refundable and non-creditable and is considered fixed consideration. We determined that the relative stand-alone selling price was $7.9 million when the license was delivered to Kyorin in January 2020. We determined that the relative standalone selling price for the free clinical trial material to be provided by us to Kyorin was $0.1 million, using the “expected cost plus a margin” approach. As of March 31, 2020, we recognized $7.9 million as license revenue under the Kyorin Agreement. We expect to recognize $0.1 million in revenue for the free clinical trial material upon delivery to Kyorin. Both the milestones and royalty payments under the Kyorin Agreement are variable consideration. Since milestone payments are binary in nature, we will use the “most-likely” method to evaluate whether the milestones should be included as revenue. We will apply constraint to these amounts until we have received notification from Kyorin that the milestone has been achieved. The royalties are dependent on future sales by Kyorin which are at the full discretion of Kyorin. Accordingly, we will apply a constraint to these amounts until the future sale sales have occurred. Hong Kong University of Science and Technology In March 2020, our subsidiary, Pangu BioPharma, together with the Hong Kong University of Science and Technology (HKUST) was awarded a grant of approximately $750,000 to build a high-throughput platform for the development of bi-specific antibodies. The two-year project is being funded by the Hong Kong Government’s Innovation and Technology Commission under the Partnership Research Program (PRP). The PRP aims to support research and development projects undertaken by companies in collaboration with local universities and public research institutions. The grant will fund approximately 50% of the total estimated project cost, with aTyr contributing the remaining 50%. The research grant agreement between Pangu BioPharma, HKUST and the Government of the Hong Kong Special Administration Region is effective April 1, 2020.

Debt, Commitments and Contingen

Debt, Commitments and Contingencies	3 Months Ended
	Mar. 31, 2020
Debt Instruments [Abstract]
Debt, Commitments and Contingencies	4. Debt, Commitments and Contingencies Term Loans In November 2016, we entered into a loan and security agreement and subsequently entered amendments (collectively, the Loan Agreement), for term loans with Silicon Valley Bank (SVB) and Solar Capital Ltd. (Solar, and together with SVB, the Lenders), to borrow up to $20.0 million issuable in three separate tranches (the Term Loans), $10.0 million of which was funded in November 2016, $5.0 million of which was funded in June 2017 and $5.0 million of which was funded in December 2017. Under the Loan Agreement, we are obligated to make interest only payments through June 1, 2018, followed by consecutive equal monthly payments of principal and interest in arrears through the maturity date of November 18, 2020. Accordingly, we started paying the Term Loans in June 2018. The Term Loans bear interest at the prime rate, as reported in The Wall Street Journal on the last date of the month preceding the month in which interest will accrue, plus 4.10%. A final payment equal to 8.75% of the funded amounts is payable when the Term Loans become due or upon the prepayment of the respective outstanding balance. We have the option to prepay the outstanding balance of the loan in full, subject to a prepayment fee ranging from 1.0% to 3.0% depending upon when the prepayment occurs, including any non-usage fees. The obligations under the Term Loans are secured by liens on our tangible personal property and we agreed to not encumber any of our intellectual property. The Term Loans include a material adverse change clause, which enables the Lenders to require immediate repayment of the outstanding debt. The material adverse change clause covers a material impairment in the perfection or priority of the Lenders’ lien in the underlying collateral or in the value of such collateral, material adverse change in business operations or condition or material impairment of our prospects for repayment of any portion of the remaining debt obligation. As of March 31, 2020, the carrying value of our Term Loans consisted of $5.3 million principal outstanding less the debt issuance costs of $0.1 million and the accretion of the final maturity payment of $1.8 million. We intend to pay our Term Loans in full, including the final maturity payment by the fourth quarter of 2020. The debt issuance costs have been recorded as a debt discount which are being accreted to interest expense over the life of the Term Loans. In connection with the first tranche, we issued warrants to the Lenders to purchase an aggregate of 3,415 shares of our common stock with an exercise price of $43.93 per share. In connection with the second tranche, we issued warrants to the Lenders to purchase an aggregate of 1,489 shares of our common stock with an exercise price of $50.37 per share. In connection with the third tranche, we issued warrants to each of the Lenders to purchase an aggregate of 1,433 shares of our common stock with an exercise price of $51.98 per share. The warrants are immediately exercisable and have a maximum contractual term of seven years. The aggregate fair value of the warrants was determined to be $0.5 million using the Black-Scholes option pricing model and was recorded as a debt discount which is being accreted to interest expense over the life of Term Loans. Facility Leases Future minimum payments under the non-cancelable facility lease and reconciliation to the operating lease liability as of March 31, 2020 were as follows (in thousands): Operating Lease 2020 $ 754 2021 1,031 2022 1,062 2023 404 Less: Amount representing interest (436 ) Present value of lease payments 2,815 Less: Current portion of operating lease liability (780 ) Long-term operating lease liability $ 2,035 For each of the three months ended March 31, 2020 and 2019, we recorded an operating lease cost of $0.2 million.

Stockholders' Equity

Stockholders' Equity	3 Months Ended
	Mar. 31, 2020
Equity [Abstract]
Stockholders' Equity	5. Stockholders’ Equity At the Market Offering Program In May 2019, we entered into a sales agreement with H.C. Wainwright & Co., LLC (Wainwright) with respect to an at-the-market offering (ATM Offering Program) under which we may offer and sell shares of our common stock having an aggregate offering price of up to $10.0 million. Wainwright is entitled to a commission at a fixed rate equal to 3% of the gross proceeds. During 2019, we sold an aggregate of 611,687 shares of common stock at an average price of $5.43 per common share for Underwritten Follow-On Public Offering In February 2020, we completed an underwritten follow-on public offering of 4,235,294 shares of our common stock at a price to the public of $4.25 per share. In March 2020, the underwriters fully exercised their option to purchase additional shares resulting in the issuance of an additional 635,294 shares of common stock. The total gross proceeds from the underwritten follow-on public offering, including the underwriters’ option to purchase additional shares, was approximately $20.7 million, before deducting underwriting discounts, commissions and offering expenses payable by us. Common Stock Reserved for Future Issuance Common stock reserved for future issuance is as follows: March 31, 2020 Common stock warrants 13,904 Common stock options and restricted stock units 489,148 Shares available under the 2015 Plan 132,725 Shares available under the 2015 ESPP 78,697 714,474 Equity Incentive Plans The following table summarizes our stock option activity under all equity incentive plans for the three months ended March 31, 2020: Number of Outstanding Stock Options Weighted Average Exercise Price Outstanding as of December 31, 2019 351,078 $ 51.34 Granted 162,434 $ 4.51 Canceled/forfeited/expired (38,932 ) $ 111.43 Outstanding as of March 31, 2020 474,580 $ 30.38 The assumptions used in the Black-Scholes option pricing model to determine the fair value of the employee stock option grants were as follows: March 31, 2020 2019 Expected term (in years) 6.02 6.02 – 6.07 Risk-free interest rate 1.5 % 2.5% – 2.6 % Expected volatility 102.2 % 100.0% – 101.0 % Expected dividend yield 0.0 % 0.0 % The following table summarizes our restricted stock unit activity under all equity incentive plans for the three months ended March 31, 2020: Number of Outstanding Restricted Stock Units Weighted Average Grant Date Fair Value Balance as of December 31, 2019 12,475 $ 9.90 Granted 5,000 $ 4.29 Released (2,679 ) $ 7.24 Forfeited (228 ) $ 11.90 Balance as of March 31, 2020 14,568 $ 8.44 Stock-based Compensation The allocation of stock-based compensation for all options, including performance options with a market condition, 2015 ESPP and restricted stock units is as follows (in thousands): March 31, 2020 2019 Research and development $ 62 $ 116 General and administrative 361 455 Total stock-based compensation expense $ 423 $ 571

Organization, Business, Basis_2

Organization, Business, Basis of Presentation and Summary of Significant Accounting Policies (Policies)	3 Months Ended
	Mar. 31, 2020
Accounting Policies [Abstract]
Organization and Business	Organization and Business aTyr Pharma, Inc. (we, us, and our) was incorporated in the state of Delaware on September 8, 2005. We are focused on the discovery and development of innovative medicines based on novel immunological pathways.
Principles of Consolidation	Principles of Consolidation Our condensed consolidated financial statements include our accounts and our 98% majority-owned subsidiary in Hong Kong, Pangu BioPharma Limited (Pangu BioPharma). All intercompany transactions and balances are eliminated in consolidation.
Unaudited Interim Financial Information	Unaudited Interim Financial Information The accompanying interim condensed consolidated financial statements are unaudited. These unaudited interim financial statements have been prepared in accordance with United States generally accepted accounting principles (GAAP) and follow the requirements of the United States Securities and Exchange Commission (SEC) for interim reporting. As permitted under those rules, certain footnotes or other financial information that are normally required by GAAP can be condensed or omitted. In our opinion, the unaudited interim financial statements have been prepared on the same basis as the audited financial statements and include all adjustments, which include only normal recurring adjustments, necessary for the fair presentation of our financial position and our results of operations and cash flows for periods presented. These statements do not include all disclosures required by GAAP and should be read in conjunction with our financial statements and accompanying notes for the fiscal year ended December 31, 2019, contained in our Annual Report on Form 10-K filed with the SEC on March 26, 2020. The results of the interim periods are not necessarily indicative of the results expected for the full fiscal year or any other interim period or any future year or period.
Reverse Stock Split	Reverse Stock Split On June 28, 2019, we filed a Certificate of Amendment to our Restated Certificate of Incorporation with the Secretary of State of the
Risks and Uncertainties	Risks and Uncertainties In December 2019, COVID-19, a novel strain of coronavirus, was first reported in Wuhan, China, has been declared a pandemic by the World Health Organization and has spread to over 100 countries, including the United States. The impact of this pandemic has been and will likely continue to be extensive in many aspects of society, which has resulted in and will continue to cause significant disruptions to the global economy, as well as businesses and capital markets around the world. Impacts to our business have included the delay in enrollment of our Phase 1b/2a clinical trial in patients with pulmonary sarcoidosis and the discontinuation of some patients in that trial, temporary closures of portions of our facilities and those of our licensees and collaborators, disruptions or restrictions on our employee's ability to travel and delays in certain research and development activities. Other potential impacts to our business include, but are not limited to disruptions to or delays in other clinical trials, third-party manufacturing supply and other operations, the potential diversion of healthcare resources away from the conduct of clinical trials to focus on pandemic concerns, interruptions or delays in the operations of the U.S. Food and Drug Administration or other regulatory authorities, and our ability to raise capital and conduct business development activities. .
Liquidity and Financial Condition	We have incurred losses and negative cash flows from operations since our inception. As of March 31, 2020, we had an accumulated deficit of $320.6 million and we expect to continue to incur net losses for the foreseeable future. We believe that our existing cash, cash equivalents and available-for-sale investments of $49.8 million as of March 31, 2020 will be sufficient to meet our anticipated cash requirements for a period of at least one year from the filing date of this Quarterly Report on Form 10-Q. We do not expect to generate any revenues from product sales unless and until we successfully complete development and obtain regulatory approval for one or more of our product candidates, which we expect will take a number of years at a minimum. If we obtain regulatory approval for any of our product candidates, we expect to incur significant commercialization expenses related to product sales, marketing, manufacturing and distribution. Accordingly, we will need to raise substantial additional capital to fund our operations. The amount and timing of our future funding requirements will depend on many factors, including, but not limited to, the pace and results of our preclinical and clinical development efforts and the timing and nature of the regulatory approval process for our product candidates. We anticipate that we will seek to fund our operations through equity offerings, grant funding, collaborations, strategic partnerships and/or licensing arrangements, and when we are closer to commercialization of our product candidates potentially through debt financings. However, we may be unable to raise additional capital or enter into such arrangements when needed on favorable terms or at all. As a result of the COVID-19 pandemic and actions taken to slow its spread, the global credit and financial markets have recently experienced extreme volatility and disruptions, including diminished liquidity and credit availability, declines in consumer confidence, declines in economic growth, increases in unemployment rates and uncertainty about economic stability. If the equity and credit markets continue to deteriorate, it may make any additional debt or equity financing more difficult, more costly and more dilutive. Our failure to raise capital or enter into applicable arrangements when needed would have a negative impact on our financial condition and ability to develop our product candidates.
Use of Estimates	Use of Estimates Our condensed consolidated financial statements are prepared in accordance with GAAP. The preparation of our condensed consolidated financial statements requires us to make estimates and assumptions that impact the reported amounts of assets, liabilities and expenses and the disclosure of contingent assets and liabilities in our condensed consolidated financial statements and accompanying notes. The most significant estimates in our condensed consolidated financial statements relate to the clinical trials and research and development expenses. Although these estimates are based on our knowledge of current events and actions we may undertake in the future, actual results may ultimately differ materially from these estimates and assumptions. Though the impact of the COVID-19 pandemic to our business and operating results presents additional uncertainty, we continue to use the best information available to us in our critical accounting estimates.
Leases	Leases We follow Accounting Standards Codification (ASC) Topic 842, Leases We elected the package of practical expedients permitted under the transition guidance within the new standard, which among other things, allowed us to exclude from our condensed consolidated balance sheets recognition of leases having a term of 12 months or less (short-term leases) and we elected to not separate lease components and non-lease components for our long-term leases. Rent expense for the operating lease is recognized on a straight-line basis over the lease term and is included in operating expenses in our condensed consolidated statements of operations.
Revenue Recognition	Revenue Recognition We evaluate our agreements under ASC Topic 606, Revenue from Contracts with Customers and ASC Topic 808, Collaborative Arrangements . . In determining the appropriate amount of revenue to be recognized as we fulfill our obligations under our agreement, we perform the following steps: (i) identification of the promised goods or services in the contract; (ii) determination of whether the promised goods or services are performance obligations including whether they are distinct in the context of the contract; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations; and (v) recognition of revenue when (or as) we satisfy each performance obligation. As part of the accounting for these arrangements, we must develop assumptions that require judgment to determine the stand-alone selling price for each performance obligation identified in the contract. We use key assumptions to determine the stand-alone selling price, which may include forecasted revenues, development timelines, reimbursement rates for personnel costs, discount rates and probabilities of technical and regulatory success. We recognize revenue in one of two ways, over time or at a point in time. We recognize revenue over time when we are executing on our performance obligation over time and our partner receives benefit over time. For example, we recognize revenue over time when we provide research and development services. We recognize revenue at a point in time when we transfer control of a distinct performance obligation to our partner. For example, if
Basic and Diluted Net Income (Loss) Per Share	Basic and Diluted Basic Net Income (Loss) Per Share Basic net income (loss) per share is calculated by dividing the net income (loss) by the weighted average number of common shares outstanding for the period, without consideration for common stock equivalents and adjusted for the weighted average number of common shares outstanding that are subject to repurchase. Diluted Net Income (Loss) Per Share For the three months ended March 31, 2020, we had net income available to common stockholders. As a result, we computed diluted net income per share using the weighted average number of common shares and dilutive common equivalent shares outstanding during the period. Dilutive common equivalent shares outstanding included 3,006 shares of restricted stock units. For the three months ended March 31, 2020, the calculation excluded the following common equivalent shares because the effect on diluted earnings per share was anti-dilutive: Common stock warrants 13,904 Common stock options and restricted stock units 486,142 Employee stock purchase plan 1,958 502,004 For the three months ended March 31, 2019, common stock from the following would have had an anti-dilutive effect on net loss per share (in common share equivalents): Class X Preferred Stock (if-converted to common stock) 587,445 Common stock warrants 477,639 Common stock options and restricted stock units 404,977 Employee stock purchase plan 1,610 1,471,671
Recent Accounting Pronouncements	Recent Accounting Pronouncements In June 2016, the Financial Accounting Standards Board (FASB) issued Accounting Standards Update (ASU) No. 2016-13, Financial Instruments – Credit Losses to provide financial statement users with more decision-useful information about the expected credit losses on financial instruments and other commitments to extend credit held by a reporting entity at each reporting date. To achieve this objective, the amendments in Topic 326 replace the incurred loss impairment methodology in current GAAP with a methodology that reflects expected credit losses and requires consideration of a broader range of reasonable and supportable information to inform credit loss estimates. Topic 326 are effective for fiscal years beginning after December 15, 2022, including interim periods within those fiscal years for small reporting companies. We are currently evaluating the impact of Topic 326 and do not expect the adoption of this guidance will have a material impact on our condensed consolidated financial position or results of operations. In December 2019, the FASB issued ASU No. 2019-12, Income Taxes Simplifying the Accounting for Income Taxes

Organization, Business, Basis_3

Organization, Business, Basis of Presentation and Summary of Significant Accounting Policies (Tables)	3 Months Ended
	Mar. 31, 2020
Accounting Policies [Abstract]
Schedule of Common Equivalent Shares Excluded for Calculation of Diluted Earning Per Share	Common stock warrants 13,904 Common stock options and restricted stock units 486,142 Employee stock purchase plan 1,958 502,004 For the three months ended March 31, 2019, common stock from the following would have had an anti-dilutive effect on net loss per share (in common share equivalents): Class X Preferred Stock (if-converted to common stock) 587,445 Common stock warrants 477,639 Common stock options and restricted stock units 404,977 Employee stock purchase plan 1,610 1,471,671

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	3 Months Ended
	Mar. 31, 2020
Fair Value Disclosures [Abstract]
Schedule of Assets Measured at Fair Value on Recurring Basis	Assets measured at fair value on a recurring basis are as follows (in thousands): Fair Value Measurements Using Total Quoted Active for Assets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) As of March 31, 2020 Assets: Current: Cash equivalents $ 34,674 $ 34,674 $ — $ — Available-for-sale investments, short-term: Asset-backed securities 3,100 — 3,100 — Commercial paper 5,076 — 5,076 — Corporate debt securities 2,200 — 2,200 — Total short-term investments 10,376 — 10,376 — Total assets measured at fair value $ 45,050 $ 34,674 $ 10,376 $ — Fair Value Measurements Using Total Quoted Active for Assets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) As of December 31, 2019 Assets: Current: Cash equivalents $ 8,248 $ 8,248 $ — $ — Available-for-sale investments, short-term: Asset-backed securities 6,304 — 6,304 — Commercial paper 7,568 — 7,568 — Corporate debt securities 8,062 — 8,062 — Total short-term investments 21,934 — 21,934 — Total assets measured at fair value $ 30,182 $ 8,248 $ 21,934 $ —
Schedule of Available-for-sale Investments	As of March 31, 2020 and December 31, 2019, available-for-sale investments are detailed as follows (in thousands): March 31, 2020 Gross Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Market Value Available-for-sale investments, short-term: Asset-backed securities $ 3,102 $ — $ (2 ) $ 3,100 Commercial paper 5,077 — — 5,077 Corporate debt securities 2,200 — (1 ) 2,199 $ 10,379 $ — $ (3 ) $ 10,376 December 31, 2019 Gross Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Market Value Available-for-sale investments, short-term: Asset-backed securities $ 6,299 $ 5 $ — $ 6,304 Commercial paper 7,568 — — 7,568 Corporate debt securities 8,057 5 — 8,062 $ 21,924 $ 10 $ — $ 21,934

Debt, Commitments and Conting_2

Debt, Commitments and Contingencies (Tables)	3 Months Ended
	Mar. 31, 2020
Debt Instruments [Abstract]
Schedule of Future Minimum Payments under Non-cancelable Operating Lease and Reconciliation to Operating Lease Liability	Future minimum payments under the non-cancelable facility lease and reconciliation to the operating lease liability as of March 31, 2020 were as follows (in thousands): Operating Lease 2020 $ 754 2021 1,031 2022 1,062 2023 404 Less: Amount representing interest (436 ) Present value of lease payments 2,815 Less: Current portion of operating lease liability (780 ) Long-term operating lease liability $ 2,035

Stockholders' Equity (Tables)

Stockholders' Equity (Tables)	3 Months Ended
	Mar. 31, 2020
Summary of Common Stock Reserved for Future Issuance	Common stock reserved for future issuance is as follows: March 31, 2020 Common stock warrants 13,904 Common stock options and restricted stock units 489,148 Shares available under the 2015 Plan 132,725 Shares available under the 2015 ESPP 78,697 714,474
Summary of Stock Option Activity	Equity Incentive Plans The following table summarizes our stock option activity under all equity incentive plans for the three months ended March 31, 2020: Number of Outstanding Stock Options Weighted Average Exercise Price Outstanding as of December 31, 2019 351,078 $ 51.34 Granted 162,434 $ 4.51 Canceled/forfeited/expired (38,932 ) $ 111.43 Outstanding as of March 31, 2020 474,580 $ 30.38
Schedule of Restricted Stock Unit Activity	The following table summarizes our restricted stock unit activity under all equity incentive plans for the three months ended March 31, 2020: Number of Outstanding Restricted Stock Units Weighted Average Grant Date Fair Value Balance as of December 31, 2019 12,475 $ 9.90 Granted 5,000 $ 4.29 Released (2,679 ) $ 7.24 Forfeited (228 ) $ 11.90 Balance as of March 31, 2020 14,568 $ 8.44
Schedule of Allocation of Stock-Based Compensation for All Options Including Performance Options with Market Condition, 2015 ESPP and Restricted Stock Units	The allocation of stock-based compensation for all options, including performance options with a market condition, 2015 ESPP and restricted stock units is as follows (in thousands): March 31, 2020 2019 Research and development $ 62 $ 116 General and administrative 361 455 Total stock-based compensation expense $ 423 $ 571
Employee Stock Option [Member]
Summary of Assumptions Used to Determine Fair Value of Employee Stock Option Grants and Performance Options with Market Condition	The assumptions used in the Black-Scholes option pricing model to determine the fair value of the employee stock option grants were as follows: March 31, 2020 2019 Expected term (in years) 6.02 6.02 – 6.07 Risk-free interest rate 1.5 % 2.5% – 2.6 % Expected volatility 102.2 % 100.0% – 101.0 % Expected dividend yield 0.0 % 0.0 %

Organization, Business, Basis_4

Organization, Business, Basis of Presentation and Summary of Significant Accounting Policies - Additional Information (Detail) - USD ($) $ in Thousands	Jun. 28, 2019	Mar. 31, 2020	Mar. 31, 2019	Dec. 31, 2019
Significant Accounting Policies [Line Items]
Reverse stock split	1-for-14
Accumulated deficit		$ 320,551		$ 322,304
Cash, cash equivalents and available-for-sale investments		$ 49,800
Shares used in computing diluted net income (loss) per share		6,884,797	2,418,674
Restricted Stock Units [Member]
Significant Accounting Policies [Line Items]
Shares used in computing diluted net income (loss) per share		3,006
Pangu BioPharma [Member] | Hong Kong [Member]
Significant Accounting Policies [Line Items]
Majority-owned subsidiary percentage		98.00%

Organization, Business, Basis_5

Organization, Business, Basis of Presentation and Summary of Significant Accounting Policies - Schedule of Common Equivalent Shares Excluded for Calculation of Diluted Earning Per Share (Detail) - shares	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Anti-dilutive securities not considered for calculation of diluted net loss per share	502,004	1,471,671
Common Stock Warrants [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Anti-dilutive securities not considered for calculation of diluted net loss per share	13,904	477,639
Common Stock Options and Restricted Stock Units [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Anti-dilutive securities not considered for calculation of diluted net loss per share	486,142	404,977
Employee Stock Purchase Plan [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Anti-dilutive securities not considered for calculation of diluted net loss per share	1,958	1,610
Class X Preferred Stock (if-converted to common stock) [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Anti-dilutive securities not considered for calculation of diluted net loss per share		587,445

Fair Value Measurements - Sched

Fair Value Measurements - Schedule of Assets Measured at Fair Value on Recurring Basis (Detail) - Fair Value, Measurements, Recurring [Member] - USD ($) $ in Thousands	Mar. 31, 2020	Dec. 31, 2019
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	$ 34,674	$ 8,248
Investments, fair value	10,376	21,934
Total assets measured at fair value	45,050	30,182
Available-for-sale [Member] | Short-term Investments [Member] | Asset-backed Securities [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments, fair value	3,100	6,304
Available-for-sale [Member] | Short-term Investments [Member] | Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments, fair value	5,076	7,568
Available-for-sale [Member] | Short-term Investments [Member] | Corporate Debt Securities [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments, fair value	2,200	8,062
Quoted Prices in Active Markets for Identical Assets (Level 1) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	34,674	8,248
Total assets measured at fair value	34,674	8,248
Significant Other Observable Inputs (Level 2) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments, fair value	10,376	21,934
Total assets measured at fair value	10,376	21,934
Significant Other Observable Inputs (Level 2) [Member] | Available-for-sale [Member] | Short-term Investments [Member] | Asset-backed Securities [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments, fair value	3,100	6,304
Significant Other Observable Inputs (Level 2) [Member] | Available-for-sale [Member] | Short-term Investments [Member] | Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments, fair value	5,076	7,568
Significant Other Observable Inputs (Level 2) [Member] | Available-for-sale [Member] | Short-term Investments [Member] | Corporate Debt Securities [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments, fair value	$ 2,200	$ 8,062

Fair Value Measurements - Sch_2

Fair Value Measurements - Schedule of Available-for-sale Investments (Detail) - Short-term Investments [Member] - USD ($) $ in Thousands	Mar. 31, 2020	Dec. 31, 2019
Schedule of Available-for-sale Securities [Line Items]
Gross Amortized Cost	$ 10,379	$ 21,924
Gross Unrealized Gains		10
Gross Unrealized Losses	(3)
Market Value	10,376	21,934
Commercial Paper [Member]
Schedule of Available-for-sale Securities [Line Items]
Gross Amortized Cost	5,077	7,568
Market Value	5,077	7,568
Asset-backed Securities [Member]
Schedule of Available-for-sale Securities [Line Items]
Gross Amortized Cost	3,102	6,299
Gross Unrealized Gains		5
Gross Unrealized Losses	(2)
Market Value	3,100	6,304
Corporate Debt Securities [Member]
Schedule of Available-for-sale Securities [Line Items]
Gross Amortized Cost	2,200	8,057
Gross Unrealized Gains		5
Gross Unrealized Losses	(1)
Market Value	$ 2,199	$ 8,062

Fair Value Measurements - Addit

Fair Value Measurements - Additional Information (Detail)	3 Months Ended
	Mar. 31, 2020Position
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale, investments in unrealized loss positions, number of positions	10
Available-for-sale, investments in unrealized loss positions, number of positions, less than twelve months	4
Maximum [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale investments effective maturity period	1 year

License Agreements and Other Ag

License Agreements and Other Agreements - Additional Information (Detail)	1 Months Ended			3 Months Ended
	Jan. 31, 2020USD ($)	May 31, 2019USD ($)	Mar. 31, 2019USD ($)Program	Mar. 31, 2020USD ($)
Research And Development Arrangement Contract To Perform For Others [Line Items]
Upfront payment received	$ 8,000,000
Revenue				$ 8,065,000
Hong Kong University of Science and Technology [Member]
Research And Development Arrangement Contract To Perform For Others [Line Items]
Grant awarded				$ 750,000
Funding of project cost, description				The grant will fund approximately 50% of the total estimated project cost, with aTyr contributing the remaining 50%. The research grant agreement between Pangu BioPharma, HKUST and the Government of the Hong Kong Special Administration Region is effective April 1, 2020.
Research Collaboration and Option Agreement [Member] | CSL Behring [Member]
Research And Development Arrangement Contract To Perform For Others [Line Items]
Number of programs | Program			4
Proceeds from research and development funded		$ 600,000
Maximum option fees receivable based on achievement of research milestones per program			$ 4,250,000
Maximum option fees receivable based on achievement of research milestones			$ 17,000,000
Termination notice period			45 days
Upfront payment received		$ 600,000
Research Collaboration and Option Agreement [Member] | CSL Behring [Member] | Collaboration Revenue [Member]
Research And Development Arrangement Contract To Perform For Others [Line Items]
Revenue				$ 200,000
Development Regulatory And Sales Milestones [Member]
Research And Development Arrangement Contract To Perform For Others [Line Items]
Maximum additional receivable based on achievement of research milestones	$ 167,000,000
Research Collaboration and License Agreement [Member] | Kyorin Pharmaceutical Co Ltd | Collaboration Revenue [Member]
Research And Development Arrangement Contract To Perform For Others [Line Items]
Stand-alone selling price of license				7,900,000
License revenue				7,900,000
Revenue expected to be recognized upon delivery of free product				$ 100,000

License Agreements and Other _2

License Agreements and Other Agreements - Additional Information (Detail 1)	Mar. 31, 2020
Research Collaboration and Option Agreement [Member] | CSL Behring [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date: 2020-01-01
Research And Development Arrangement Contract To Perform For Others [Line Items]
Performance obligations period	45 days

Debt, Commitments and Conting_3

Debt, Commitments and Contingencies - Additional Information (Detail)	1 Months Ended			3 Months Ended
	Dec. 31, 2017USD ($)$ / sharesshares	Jun. 30, 2017USD ($)$ / sharesshares	Nov. 30, 2016USD ($)Tranche$ / sharesshares	Mar. 31, 2020USD ($)	Mar. 31, 2019USD ($)
Debt Instrument [Line Items]
Loan and security agreement, payment term				Issuable in three separate tranches (the Term Loans), $10.0 million of which was funded in November 2016, $5.0 million of which was funded in June 2017 and $5.0 million of which was funded in December 2017.
Operating lease, cost				$ 200,000	$ 200,000
Operating lease, weighted average remaining lease term				3 years 2 months 12 days
Operating lease, weighted average discount rate				9.60%
Silicon Valley Bank and Solar Capital, Ltd. [Member]
Debt Instrument [Line Items]
Available credit under loan and security agreement			$ 20,000,000
Number of tranches | Tranche			3
Term loan, principal outstanding before deducting debt issuance cost				$ 5,300,000
Term loan, debt issuance costs				100,000
Accretion Of Final Payment Of Debt Instrument				$ 1,800,000
Warrants expiration year				7 years
Aggregate fair value of warrants using black scholes option pricing model	$ 500,000
Silicon Valley Bank and Solar Capital, Ltd. [Member] | Term Loans Tranche One [Member]
Debt Instrument [Line Items]
Available credit under loan and security agreement			$ 10,000,000
Loan and security agreement funded date			Nov. 30, 2016
Exercise price of warrant per share | $ / shares			$ 43.93
Silicon Valley Bank and Solar Capital, Ltd. [Member] | Term Loans Tranche One [Member] | Common Stock [Member]
Debt Instrument [Line Items]
Warrants to purchase number of common stock, shares | shares			3,415
Silicon Valley Bank and Solar Capital, Ltd. [Member] | Term Loans Tranche Two [Member]
Debt Instrument [Line Items]
Available credit under loan and security agreement		$ 5,000,000
Loan and security agreement funded date		Jun. 30, 2017
Exercise price of warrant per share | $ / shares		$ 50.37
Silicon Valley Bank and Solar Capital, Ltd. [Member] | Term Loans Tranche Two [Member] | Common Stock [Member]
Debt Instrument [Line Items]
Warrants to purchase number of common stock, shares | shares		1,489
Silicon Valley Bank and Solar Capital, Ltd. [Member] | Term Loans Tranche Three [Member]
Debt Instrument [Line Items]
Available credit under loan and security agreement	$ 5,000,000
Loan and security agreement funded date	Dec. 31, 2017
Exercise price of warrant per share | $ / shares	$ 51.98
Silicon Valley Bank and Solar Capital, Ltd. [Member] | Term Loans Tranche Three [Member] | Common Stock [Member]
Debt Instrument [Line Items]
Warrants to purchase number of common stock, shares | shares	1,433
Loan Amendment Agreement with SVB and Solar [Member]
Debt Instrument [Line Items]
Loan and security agreement, payment term				Under the Loan Agreement, we are obligated to make interest only payments through June 1, 2018, followed by consecutive equal monthly payments of principal and interest in arrears through the maturity date of November 18, 2020.
Maturity date				Nov. 18, 2020
Percentage of funded amounts for final payment			8.75%
Loan Amendment Agreement with SVB and Solar [Member] | Prime Rate [Member]
Debt Instrument [Line Items]
Interest rate spread on variable rate			4.10%
Loan Amendment Agreement with SVB and Solar [Member] | Minimum [Member]
Debt Instrument [Line Items]
Prepayment fee percentage			1.00%
Loan Amendment Agreement with SVB and Solar [Member] | Maximum [Member]
Debt Instrument [Line Items]
Prepayment fee percentage			3.00%

Debt, Commitments and Conting_4

Debt, Commitments and Contingencies - Schedule of Future Minimum Payments under Non-cancelable Operating Lease and Reconciliation to Operating Lease Liability (Detail) - USD ($) $ in Thousands	Mar. 31, 2020	Dec. 31, 2019
Leases Operating [Abstract]
2020	$ 754
2021	1,031
2022	1,062
2023	404
Less: Amount representing interest	(436)
Present value of lease payments	2,815
Less: Current portion of operating lease liability	(780)	$ (755)
Long-term operating lease liability	$ 2,035	$ 2,239

Stockholders' Equity - Addition

Stockholders' Equity - Additional Information (Detail) - USD ($)	1 Months Ended	3 Months Ended
	Feb. 29, 2020	Mar. 31, 2020	Mar. 10, 2020	May 31, 2019
ATM Offering Program [Member] | H.C. Wainwright & Co., LLC [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Net proceeds from issuance of common stock		$ 3,000,000
Commission rate equal to gross proceeds				3.00%
ATM Offering Program [Member] | Sale Agreement [Member] | Maximum [Member] | H.C. Wainwright & Co., LLC [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Agreed upon value of sale of common stock per transaction				$ 10,000,000
ATM Offering Program [Member] | Common Stock [Member] | H.C. Wainwright & Co., LLC [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Shares issued during the period		611,687
Shares issued, price per share		$ 5.43
Public Offering [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Net proceeds from issuance of common stock	$ 20,700,000
Public Offering [Member] | Common Stock [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Shares issued during the period	4,235,294
Shares issued, price per share	$ 4.25
Issuance of additional share of common stock			635,294

Stockholders' Equity - Summary

Stockholders' Equity - Summary of Common Stock Reserved for Future Issuance (Detail)	Mar. 31, 2020shares
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Common stock reserved for future issuance	714,474
Common Stock Warrants [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Common stock reserved for future issuance	13,904
Common Stock Options and Restricted Stock Units [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Common stock reserved for future issuance	489,148
Shares Available Under the 2015 Plan [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Common stock reserved for future issuance	132,725
Shares Available Under the 2015 ESPP [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Common stock reserved for future issuance	78,697

Stockholders' Equity - Summar_2

Stockholders' Equity - Summary of Stock Option Activity (Detail)	3 Months Ended
	Mar. 31, 2020$ / sharesshares
Disclosure Of Compensation Related Costs Sharebased Payments [Abstract]
Number of Outstanding Stock Options, Beginning Balance | shares	351,078
Number of Outstanding Stock Options, Granted | shares	162,434
Number of Outstanding Stock Options, Canceled/forfeited/expired | shares	(38,932)
Number of Outstanding Stock Options, Ending Balance | shares	474,580
Weighted Average Exercise Price, Beginning Balance | $ / shares	$ 51.34
Weighted Average Exercise Price, Granted | $ / shares	4.51
Weighted Average Exercise Price, Canceled/forfeited/expired | $ / shares	111.43
Weighted Average Exercise Price, Ending Balance | $ / shares	$ 30.38

Stockholders' Equity - Summar_3

Stockholders' Equity - Summary of Assumptions Used to Determine Fair Value of Employee Stock Option Grants, Employee Stock Purchase Plan and Performance Options with Market Condition (Detail) - Employee Stock Option [Member]	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Expected term (in years)	6 years 7 days
Risk-free interest rate	1.50%
Risk-free interest rate, minimum		2.50%
Risk-free interest rate, maximum		2.60%
Expected volatility	102.20%
Expected volatility, minimum		100.00%
Expected volatility, maximum		101.00%
Expected dividend yield	0.00%	0.00%
Minimum [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Expected term (in years)		6 years 7 days
Maximum [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Expected term (in years)		6 years 25 days

Stockholders' Equity - Schedule

Stockholders' Equity - Schedule of Restricted Stock Unit Activity (Detail) - Restricted Stock Units [Member]	3 Months Ended
	Mar. 31, 2020$ / sharesshares
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Number of Outstanding Restricted Stock Units, Beginning Balance | shares	12,475
Number of Outstanding Restricted Stock Units, Granted | shares	5,000
Number of Outstanding Restricted Stock Units, Released | shares	(2,679)
Number of Outstanding Restricted Stock Units, Forfeited | shares	(228)
Number of Outstanding Restricted Stock Units, Ending Balance | shares	14,568
Weighted Average Grant Date Fair Value, Beginning Balance | $ / shares	$ 9.90
Weighted Average Grant Date Fair Value, Granted | $ / shares	4.29
Weighted Average Grant Date Fair Value, Released | $ / shares	7.24
Weighted Average Grant Date Fair Value, Forfeited | $ / shares	11.90
Weighted Average Grant Date Fair Value, Ending Balance | $ / shares	$ 8.44

Stockholders' Equity - Schedu_2

Stockholders' Equity - Schedule of Allocation of Stock-Based Compensation for All Options 2015 ESPP and Restricted Stock Units (Detail) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2020	Mar. 31, 2019
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Total stock-based compensation expense	$ 423	$ 571
Research and Development Expense [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Total stock-based compensation expense	62	116
General and Administrative Expense [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Total stock-based compensation expense	$ 361	$ 455