# EDGAR Filing Document

**Accession Number:** 0001339970
**File Stem:** 0001339970-25-000013
**Filing Date:** 2025-8
**Character Count:** 23010
**Document Hash:** 8005c59d7e42096c798bc8a224d84c5a
**Contains OCR:** False
**Source Format:** 

## Filing Content

## Filing Summary
**0001339970-25-000013.hdr.sgml**: 20250807

**ACCESSION NUMBER**: 0001339970-25-000013

**CONFORMED SUBMISSION TYPE**: S-8

**PUBLIC DOCUMENT COUNT**: 16

**FILED AS OF DATE**: 20250807

**DATE AS OF CHANGE**: 20250807

**EFFECTIVENESS DATE**: 20250807

**FILER**: 

**COMPANY DATA:**
- **COMPANY CONFORMED NAME:** aTYR PHARMA INC
- **CENTRAL INDEX KEY:** 0001339970
- **STANDARD INDUSTRIAL CLASSIFICATION:** BIOLOGICAL PRODUCTS (NO DIAGNOSTIC SUBSTANCES) [2836]
- **ORGANIZATION NAME:** 03 Life Sciences
- **EIN:** 203435077
- **STATE OF INCORPORATION:** DE
- **FISCAL YEAR END:** 1231

**FILING VALUES:**
- **FORM TYPE:** S-8
- **SEC ACT:** 1933 Act
- **SEC FILE NUMBER:** 333-289364
- **FILM NUMBER:** 251194522

**BUSINESS ADDRESS:**
- **STREET 1:** 10240 SORRENTO VALLEY ROAD
- **STREET 2:** SUITE 300
- **CITY:** SAN DIEGO
- **STATE:** CA
- **ZIP:** 92121
- **BUSINESS PHONE:** 8587318389

**MAIL ADDRESS:**
- **STREET 1:** 10240 SORRENTO VALLEY ROAD
- **STREET 2:** SUITE 300
- **CITY:** SAN DIEGO
- **STATE:** CA
- **ZIP:** 92121

**As filed with the U.S. Securities and Exchange Commission on August 7, 2025**

**Registration No. 333-** 

**UNITED STATES**

**SECURITIES AND EXCHANGE COMMISSION**

**Washington, D.C. 20549** 

**FORM S-8** 

**REGISTRATION STATEMENT** 

***UNDER*** 

***THE SECURITIES ACT OF 1933***

**ATYR PHARMA, INC.** 

(Exact name of registrant as specified in its charter)

---

| | |
|:---|:---|
| **Delaware** | **20-3435077** |
| (State or other jurisdiction of<br>incorporation or organization) | (I.R.S. Employer<br>Identification No.) |

---

**10240 Sorrento Valley Road, Suite 300**

**San Diego, CA 92121**

(Address of Principal Executive Offices) (Zip Code)

**ATYR PHARMA, INC. 2015 STOCK OPTION AND INCENTIVE PLAN, AS AMENDED**

**ATYR PHARMA, INC. 2022 INDUCEMENT PLAN, AS AMENDED** 

(Full titles of the plans)

**Sanjay S. Shukla, M.D., M.S.**

**President, Chief Executive Officer and Director** 

**10240 Sorrento Valley Road, Suite 300** 

**San Diego, CA 92121**

**(858) 731-8389**

(Name and address of agent for service) (Telephone number, including area code, of agent for service)

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company or an emerging growth company. See the definitions of "large accelerated filer," "accelerated filer," "smaller reporting company," and "emerging growth company" in Rule 12b-2 of the Exchange Act.

---

| | | | |
|:---|:---|:---|:---|
| Large accelerated filer | ☐ | Accelerated filer | ☐ |
| Non-accelerated filer | ☒  | Smaller reporting company | ☒ |
|  |  | Emerging growth company | ☐ |

---

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 7(a)(2)(B) of the Securities Act. 

------

**EXPLANATORY NOTE**

This Registration Statement on Form S-8 (the "***Registration Statement***") is being filed by aTyr Pharma, Inc. (the "***Registrant***") for the purpose of registering an aggregate of 5,300,000 shares of the Registrant's common stock, par value $0.001 per share ("***Common Stock***"), consisting of:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•5,000,000 additional shares of Common Stock issuable pursuant to the Registrant's 2015 Stock Option and Incentive Plan, as amended (the "***2015 Plan***"), pursuant to an amendment to the 2015 Plan approved by the stockholders of the Registrant on May 1, 2025; and

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•300,000 additional shares of Common Stock issuable pursuant to the Registrant's 2022 Inducement Plan, as amended (the "***Inducement Plan***"), for an aggregate of 600,000 shares of Common Stock issuable under the Inducement Plan, pursuant to approval of the Compensation Committee of the Registrant's Board of Directors on March 21, 2025.

**INCORPORATION OF DOCUMENTS BY REFERENCE**

The Registrant previously registered shares of its Common Stock for issuance under the 2015 Plan under Registration Statements on Form S-8 filed with the Securities and Exchange Commission (the "***Commission***") on [<u>May 7, 2015</u>](https://www.sec.gov/Archives/edgar/data/1339970/000119312515177251/d921783ds8.htm) (File No. 333-203955), [<u>April 1, 2016</u>](https://www.sec.gov/Archives/edgar/data/1339970/000156459016015797/life-s8_20160401.htm) (File No. 333-210543), [<u>March 22, 2017</u>](https://www.sec.gov/Archives/edgar/data/1339970/000156459017005005/life-s8.htm) (File No. 333-216880), [<u>March 23, 2018</u>](https://www.sec.gov/Archives/edgar/data/1339970/000156459018006614/life-s8.htm) (File No. 333-223865), [<u>May 20, 2019</u>](https://www.sec.gov/Archives/edgar/data/1339970/000156459019019755/life-s8.htm) (File No. 333-231594), [<u>August 18, 2020</u>](https://www.sec.gov/Archives/edgar/data/1339970/000156459020040458/life-s8.htm) (File No. 333-248090), [<u>May 14, 2021</u>](https://www.sec.gov/Archives/edgar/data/1339970/000156459021028035/life-s8.htm) (File No. 333- 256145), [<u>May 11, 2022</u>](https://www.sec.gov/Archives/edgar/data/1339970/000156459022019562/life-s8.htm) (File No. 333-264866), [<u>August 10, 2023</u>](https://www.sec.gov/Archives/edgar/data/1339970/000095017023041306/2023_s-8.htm) (File No. 333-273876) and [<u>August 13, 2024</u>](https://www.sec.gov/Archives/edgar/data/1339970/000095017024096360/2024_s-8.htm) (File No. 333-281525).

The Registrant previously registered shares of its Common Stock for issuance under the Inducement Plan under a Registration Statement on Form S-8 filed with the Commission on [<u>May 11, 2022</u>](https://www.sec.gov/Archives/edgar/data/1339970/000156459022019562/life-s8.htm) (File No. 333-264866).

This Registration Statement is being filed for the purpose of registering additional securities of the same class as other securities for which Registration Statements of the Registrant on Form S-8 relating to the same employee benefit plans are effective.

Pursuant to General Instruction E to Form S-8, this Registration Statement hereby incorporates by reference the contents of the registration statements referenced above and the description of the Registrant's Common Stock which is contained in a Registration Statement on [<u>Form 8-A</u>](https://www.sec.gov/Archives/edgar/data/1339970/000119312515173955/d917258d8a12b.htm) filed with the Commission on May 6, 2015 (File No. 001-37378) under Section 12(b) of the Securities Exchange Act of 1934, as amended, including any amendment or report filed for the purpose of updating such description, including [<u>Exhibit 4.6</u>](https://www.sec.gov/Archives/edgar/data/1339970/000095017024031584/life-ex4_6.htm) to the Registrant's Annual Report on Form 10-K for the fiscal year ended December 31, 2023, as filed with the Commission on March 14, 2024.

------

**Item 8. Exhibits.**

The exhibits to this Registration Statement are listed below:

---

| | | | | | |
|:---|:---|:---|:---|:---|:---|
|  |  |  | &nbsp;&nbsp;**Incorporated by Reference** | &nbsp;&nbsp;**Incorporated by Reference** |  |
| &nbsp;&nbsp;&nbsp;&nbsp;**Exhibit**<br>**Number** | **Exhibit Title** | &nbsp;&nbsp;**Form** | &nbsp;&nbsp;**File No.** | &nbsp;&nbsp;**Exhibit** | &nbsp;&nbsp;**Filing Date** |
| 4.1 | [<u>Restated Certificate of Incorporation of the Registrant</u>](https://www.sec.gov/Archives/edgar/data/1339970/000095017022024724/life-ex3_1.htm) | &nbsp;&nbsp;10-Q | &nbsp;&nbsp;001-37378 | &nbsp;&nbsp;3.1 | &nbsp;&nbsp;November 14, 2022 |
| 4.2 | [<u>Certificate of Amendment to Restated Certificate of Incorporation of the Registrant</u>](https://www.sec.gov/Archives/edgar/data/1339970/000156459019024064/life-ex31_7.htm) | &nbsp;&nbsp;8-K | &nbsp;&nbsp;001-37378 | &nbsp;&nbsp;3.1 | &nbsp;&nbsp;June 28, 2019 |
| 4.3 | [<u>Certificate of Amendment to Restated Certificate of Incorporation of the Registrant</u>](https://www.sec.gov/Archives/edgar/data/1339970/000156459020024729/life-ex33_130.htm) | &nbsp;&nbsp;10-Q | &nbsp;&nbsp;001-37378 | &nbsp;&nbsp;3.3 | &nbsp;&nbsp;May 12, 2020 |
| 4.4 | [<u>Certificate of Amendment to Restated Certificate of Incorporation of the Registrant</u>](https://www.sec.gov/Archives/edgar/data/1339970/000156459021023319/life-ex31_14.htm) | &nbsp;&nbsp;8-K | &nbsp;&nbsp;001-37378 | &nbsp;&nbsp;3.1 | &nbsp;&nbsp;May 4, 2021 |
| 4.5 | [<u>Certificate of Amendment to Restated Certificate of Incorporation of the Registrant</u>](https://www.sec.gov/Archives/edgar/data/1339970/000156459022016548/life-ex31_8.htm) | &nbsp;&nbsp;8-K | &nbsp;&nbsp;001-37378 | &nbsp;&nbsp;3.1 | &nbsp;&nbsp;April 29, 2022 |
| 4.6 | [<u>Certificate of Amendment to Restated Certificate of Incorporation of the Registrant</u>](https://www.sec.gov/Archives/edgar/data/1339970/000095017023023257/life-ex3_1.htm) | &nbsp;&nbsp;8-K | &nbsp;&nbsp;001-37378 | &nbsp;&nbsp;3.1 | &nbsp;&nbsp;May 19, 2023 |
| 4.7 | [<u>Amended and Restated Bylaws of the Registrant</u>](https://www.sec.gov/Archives/edgar/data/1339970/000095017022024724/life-ex3_6.htm) | &nbsp;&nbsp;10-Q | &nbsp;&nbsp;001-37378 | &nbsp;&nbsp;3.6 | &nbsp;&nbsp;November 14, 2022 |
| 4.8 | [<u>Specimen</u> <u>Common</u> <u>Stock</u> <u>Certificate</u>](https://www.sec.gov/Archives/edgar/data/1339970/000119312515148013/d819057dex41.htm) | &nbsp;&nbsp;S-1/A | &nbsp;&nbsp;333-203272 | &nbsp;&nbsp;4.1 | &nbsp;&nbsp;April 27, 2015 |
| 5.1  | [<u>Opinion of Cooley LLP</u>](atyr-ex5_1.htm) | &nbsp;&nbsp;— | &nbsp;&nbsp;— | &nbsp;&nbsp;— | &nbsp;&nbsp;Filed herewith |
| 23.1 | [<u>Consent of Cooley LLP (included in Exhibit 5.1)</u>](atyr-ex5_1.htm) | &nbsp;&nbsp;— | &nbsp;&nbsp;— | &nbsp;&nbsp;— | &nbsp;&nbsp;Filed herewith |
| 23.2 | [<u>Consent of Independent Registered Public Accounting Firm</u>](atyr-ex23_2.htm) | &nbsp;&nbsp;— | &nbsp;&nbsp;— | &nbsp;&nbsp;— | &nbsp;&nbsp;Filed herewith |
| 24.1 | [<u>Power of Attorney (included on the signature page hereto)</u>](#powerofattorney) | &nbsp;&nbsp;— | &nbsp;&nbsp;— | &nbsp;&nbsp;— | &nbsp;&nbsp;Filed herewith |
| 99.1 | [<u>aTyr Pharma, Inc. 2015 Stock Option and Incentive Plan, as amended</u>](https://www.sec.gov/Archives/edgar/data/1339970/000095017025064413/atyr-ex10_1.htm) | &nbsp;&nbsp;8-K | &nbsp;&nbsp;001-37378 | &nbsp;&nbsp;10.1 | &nbsp;&nbsp;May 6, 2025 |
| 99.2 | [<u>aTyr Pharma, Inc. 2022 Inducement Plan, as amended</u>](https://www.sec.gov/Archives/edgar/data/1339970/000133997025000009/atyr-ex10_2.htm) | &nbsp;&nbsp;10-Q | &nbsp;&nbsp;001-37378 | &nbsp;&nbsp;10.2 | &nbsp;&nbsp;August 7, 2025 |
| 107 | [<u>Filing Fee Table</u>](atyr_exfilingfees.htm) | &nbsp;&nbsp;— | &nbsp;&nbsp;— | &nbsp;&nbsp;— | &nbsp;&nbsp;Filed herewith |

---

------

**SIGNATURES**

Pursuant to the requirements of the Securities Act of 1933, the registrant certifies that it has reasonable grounds to believe that it meets all of the requirements for filing on Form S-8 and has duly caused this registration statement to be signed on its behalf by the undersigned, thereunto duly authorized, in the City of San Diego, State of California, this 7<sup>th</sup> day of August, 2025.

---

| | |
|:---|:---|
| **ATYR PHARMA, INC.** | **ATYR PHARMA, INC.** |
| By: | /s/ Sanjay S. Shukla |
|  | Sanjay S. Shukla, M.D., M.S. |
|  | *President, Chief Executive Officer and Director* |

---

**POWER OF ATTORNEY AND SIGNATURES**

We, the undersigned officers and directors of aTyr Pharma, Inc., hereby severally constitute and appoint Sanjay S. Shukla, M.D., M.S. and Jill M. Broadfoot, and each of them singly (with full power to each of them to act alone), our true and lawful attorneys-in-fact and agents, with full power of substitution and resubstitution in each of them for their and in their name, place and stead, and in any and all capacities, to sign for us and in our names in the capacities indicated below any and all amendments (including post-effective amendments) to this registration statement on Form S-8, and to file the same, with all exhibits thereto and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and every act and thing requisite or necessary to be done in and about the premises, as full to all intents and purposes as he or she might or could do in person, hereby ratifying and confirming all that said attorneys-in-fact and agents or any of them, or their or his or her substitute or substitutes, may lawfully do or cause to be done by virtue hereof.

Pursuant to the requirements of the Securities Act of 1933, this registration statement has been signed by the following persons in the capacities and on the date indicated below.

---

| | | |
|:---|:---|:---|
| **Signature** | **Title** | **Date** |
| /s/ Sanjay S. Shukla | &nbsp;&nbsp;&nbsp;President, Chief Executive Officer and Director | August 7, 2025 |
| Sanjay S. Shukla, M.D., M.S. | &nbsp;&nbsp;&nbsp;*(Principal Executive Officer)* |  |
| /s/ Jill M. Broadfoot  | &nbsp;&nbsp;&nbsp;Chief Financial Officer | August 7, 2025 |
| Jill M. Broadfoot | &nbsp;&nbsp;&nbsp;*(Principal Financial and Accounting Officer)* |  |
| /s/ Timothy P. Coughlin | Chairman of the Board  | August 7, 2025 |
| Timothy P. Coughlin |  |  |
| /s/ Eric Benevich | Director | August 7, 2025 |
| Eric Benevich |  |  |
| /s/ Jane A. Gross | &nbsp;&nbsp;&nbsp;Director | August 7, 2025 |
| Jane A. Gross, Ph.D. |  |  |
| /s/ Svetlana Lucas | &nbsp;&nbsp;&nbsp;Director | August 7, 2025 |
| Svetlana Lucas, Ph.D. |  |  |
| /s/ Paul Schimmel | &nbsp;&nbsp;&nbsp;Director | August 7, 2025 |
| Paul Schimmel, Ph.D. |  |  |
| /s/ Sara L. Zaknoen | &nbsp;&nbsp;&nbsp;Director | August 7, 2025 |
| Sara L. Zaknoen, M.D. |  |  |

---

------

## Exhibit 5.1

![gfx54294278_0.gif](gfx54294278_0.gif)

306644959 v3

![img54294278_0.jpg](img54294278_0.jpg)

Exhibit 5.1

Charles J. Bair

+1 858 550 6142

cbair@cooley.com

August 8, 2025

aTyr Pharma, Inc.

10240 Sorrento Valley Road, Suite 300

San Diego, CA 92121

Ladies and Gentlemen:

We have acted as counsel to aTyr Pharma, Inc., a Delaware corporation (the "***Company***"), in connection with the filing by the Company of a registration statement on Form S-8 (the "***Registration Statement***") with the Securities and Exchange Commission (the "***Commission***") covering the offering by the Company of up to 5,300,000 shares (the "***Shares***") of its common stock, $0.001 par value per share ("***Common Stock***"), consisting of (i) 5,000,000 shares of Common Stock issuable pursuant to the Company's 2015 Stock Option and Incentive Plan, as amended (the "***2015 Stock Plan***"); and (ii) 300,000 shares of Common Stock issuable pursuant to the Company's 2022 Inducement Plan, as amended (together with the 2015 Stock Plan, the "***Plans***").

In connection with this opinion, we have examined and relied upon the Registration Statement and the related prospectuses, the Plans, the Company's certificate of incorporation and bylaws, each as currently in effect, and such other records, documents, certificates, memoranda and instruments as in our judgment are necessary or appropriate to enable us to render the opinion expressed below. We have assumed the genuineness of all signatures, the authenticity of all documents submitted to us as originals, the conformity to originals of all documents submitted to us as copies, the accuracy, completeness and authenticity of certificates of public officials, and the due authorization, execution and delivery of all documents by all persons other than by the Company. As to certain factual matters, we have relied upon a certificate of an officer of the Company and have not independently verified such matters.

Our opinion is expressed only with respect to the General Corporation Law of the State of Delaware. We express no opinion to the extent that any other laws are applicable to the subject matter hereof and express no opinion and provide no assurance as to compliance with any federal or state securities law, rule or regulation.

On the basis of the foregoing, and in reliance thereon, we are of the opinion that the Shares, when sold and issued in accordance with the Plans, and the Registration Statement and related prospectuses, will be validly issued, fully paid and nonassessable (except as to Shares issued pursuant to deferred payment arrangements, which will be fully paid and nonassessable when such deferred payments are made in full).

This opinion is limited to the matters expressly set forth in this letter, and no opinion has been or should be implied, or may be inferred, beyond the matters expressly stated. This opinion speaks only as to law and facts in effect or existing as of the date hereof, and we have no obligation or responsibility to update or supplement this letter to reflect any facts or circumstances that may hereafter come to our attention or any changes in law that may hereafter occur.

We consent to the filing of this opinion as an exhibit to the Registration Statement. In giving such consent, we do not thereby admit that we are in the category of persons whose consent is required under Section 7 of the Securities Act of 1933, as amended, or the rules and regulations of the Commission thereunder.

Sincerely,

Cooley LLP

By: /s/ Charles J. Bair<u>.</u>

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Charles J. Bair

Cooley LLP 10265 Science Center Drive San Diego, CA 92121<br>T: (858) 550-6000 F: (858) 550-6420 cooley.com

------

## Exhibit 23.2

**Exhibit 23.2**

**Consent of Independent Registered Public Accounting Firm**

We consent to the incorporation by reference in the Registration Statement (Form S-8) pertaining to the aTyr Pharma, Inc. 2015 Stock Option and Incentive Plan, as amended and the aTyr Pharma, Inc. 2022 Inducement Plan, as amended of our report dated March 13, 2025, with respect to the consolidated financial statements of aTyr Pharma, Inc. included in its Annual Report (Form 10-K) for the year ended December 31, 2024, filed with the Securities and Exchange Commission.

/s/ Ernst & Young LLP

San Diego, California

August 7, 2025

------

## Ex-Filing

?xml version='1.0' encoding='ASCII'? EX-FILING FEES

**Calculation of** Filing Fee **Table**

**Form** S-8

(Form Type)

aTyr Pharma, Inc.

(Exact Name of Registrant as Specified in its Charter)

<u>Table 1: Newly Registered Securities</u>

---

| | | | | | | | | |
|:---|:---|:---|:---|:---|:---|:---|:---|:---|
|  | &nbsp;&nbsp;&nbsp;**Security Type** | &nbsp;&nbsp;&nbsp;**Security Class Title** | &nbsp;&nbsp;&nbsp;**Fee Calculation Rule** | &nbsp;&nbsp;&nbsp;**Amount Registered** | &nbsp;&nbsp;&nbsp;**Proposed Maximum Offering Price Per Unit** | &nbsp;&nbsp;&nbsp; **Maximum Aggregate Offering Price** | &nbsp;&nbsp;&nbsp;**Fee Rate** | &nbsp;&nbsp;&nbsp;**Amount of Registration Fee** |
| &nbsp;&nbsp;1 | &nbsp;&nbsp;Equity | &nbsp;&nbsp;2015 Stock Option and Incentive Plan, as amended<br>Common Stock, par value $0.001 per share<br>| &nbsp;&nbsp;Other | &nbsp;&nbsp;5000000 | &nbsp;&nbsp;$4.61 | &nbsp;&nbsp;$23050000 | &nbsp;&nbsp;0.0001531 | &nbsp;&nbsp;$3529 |
| &nbsp;&nbsp;2 | &nbsp;&nbsp;Equity | &nbsp;&nbsp;2022 Inducement Plan, as amended<br>Common Stock, par value $0.001 per share<br>| &nbsp;&nbsp;Other | &nbsp;&nbsp;300000 | &nbsp;&nbsp;$4.61 | &nbsp;&nbsp;$1383000 | &nbsp;&nbsp;0.0001531 | &nbsp;&nbsp;$212 |
|  | &nbsp;&nbsp;&nbsp;&nbsp;**Total Offering Amounts** | &nbsp;&nbsp;&nbsp;&nbsp;**Total Offering Amounts** | &nbsp;&nbsp;&nbsp;&nbsp;**Total Offering Amounts** | &nbsp;&nbsp;&nbsp;&nbsp;**Total Offering Amounts** |  | &nbsp;&nbsp;$24433000 |  | &nbsp;&nbsp;$3741 |
|  | &nbsp;&nbsp;&nbsp;&nbsp;**Total Fee Offsets** | &nbsp;&nbsp;&nbsp;&nbsp;**Total Fee Offsets** | &nbsp;&nbsp;&nbsp;&nbsp;**Total Fee Offsets** | &nbsp;&nbsp;&nbsp;&nbsp;**Total Fee Offsets** |  |  |  | &nbsp;&nbsp;— |
|  | &nbsp;&nbsp;&nbsp;&nbsp;**Net Fee Due** | &nbsp;&nbsp;&nbsp;&nbsp;**Net Fee Due** | &nbsp;&nbsp;&nbsp;&nbsp;**Net Fee Due** | &nbsp;&nbsp;&nbsp;&nbsp;**Net Fee Due** |  |  |  | &nbsp;&nbsp;$3741 |

---

**Offering Note**

1 Pursuant to Rule 416(a) under the Securities Act of 1933, as amended (the "***Securities Act***"), this Registration Statement on Form S-8 (this "***Registration Statement***") shall also cover any additional shares of common stock, par value $0.001 per share ("***Common Stock***"), of aTyr Pharma, Inc. (the "***Registrant***") that become issuable under the aTyr Pharma, Inc. 2015 Stock Option and Incentive Plan, as amended (the "***2015 Plan***"), by reason of any stock dividend, stock split, recapitalization or other similar transaction.

The proposed maximum offering price per unit and proposed maximum aggregate offering price are estimated pursuant to Rule 457(h) and Rule 457(c) under the Securities Act solely for purposes of calculating the registration fee, which is calculated using the average of the high and low prices of the Common Stock on August 1, 2025, as reported on the Nasdaq Capital Market, which date is within five business days prior to the filing of this Registration Statement.

The number of shares being registered represents 5,000,000 additional shares of Common Stock reserved and available for issuance under the 2015 Plan, as approved by the Registrant's stockholders at its annual meeting of stockholders on May 1, 2025 (the "***2025 Annual Meeting***"). At the 2025 Annual Meeting, the Registrant's stockholders approved an amendment to the 2015 Plan to increase the maximum number of shares of Common Stock reserved and available for issuance under the 2015 Plan by 5,000,000 to 15,719,300.

2 Pursuant to Rule 416(a) under the Securities Act, this Registration Statement shall also cover any additional shares of Common Stock that become issuable under the aTyr Pharma, Inc. 2022 Inducement Plan, as amended (the "***Inducement Plan***"), by reason of any stock dividend, stock split, recapitalization or other similar transaction.

The proposed maximum offering price per unit and proposed maximum aggregate offering price are estimated pursuant to Rule 457(h) and Rule 457(c) under the Securities Act solely for purposes of calculating the registration fee, which is calculated using the average of the high and low prices of the Common Stock on August 1, 2025, as reported on the Nasdaq Capital Market, which date is within five business days prior to the filing of this Registration Statement.

------

The number of shares being registered represents 300,000 additional shares of Common Stock reserved and available for issuance under the Inducement Plan, for an aggregate of 600,000 shares of Common Stock issuable under the Inducement Plan, pursuant to approval of the Compensation Committee of the Registrant's Board of Directors on March 21, 2025.

------