Document:

EX-4.3

 Exhibit 4.3 

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR ANY
APPLICABLE STATE SECURITIES LAWS, AND EXCEPT AND PURSUANT TO THE PROVISIONS OF ARTICLE 5 BELOW, MAY NOT BE SOLD, OFFERED OR OTHERWISE TRANSFERRED WITHOUT AN EFFECTIVE REGISTRATION THEREOF UNDER THE ACT AND ANY APPLICABLE STATE SECURITIES LAWS,
OR PURSUANT TO RULE 144 OR AN EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF THE ACT AND ANY APPLICABLE STATE SECURITIES LAWS. 

WARRANT TO PURCHASE STOCK 
  

			
	Corporation:	  	ATYR PHARMA, INC., a Delaware corporation
	Number of Shares:	  	15,957, subject to adjustment as set forth below
	Class of Stock:	  	Series C Preferred Stock
	Initial Exercise Price:	  	$0.94 per share
	Issue Date:	  	March 18, 2011
	Expiration Date:	  	March 18, 2021 (Subject to Section 4.1)

 THIS WARRANT TO PURCHASE STOCK (this “WARRANT”) CERTIFIES THAT, for good and valuable consideration,
the receipt of which is hereby acknowledged, COMERICA BANK, a Texas banking association, or its assignee (“Holder”), is entitled to purchase the number of fully paid and nonassessable shares of the class of securities (the
“Shares”) of ATYR PHARMA, INC. (the “Company”) at the initial exercise price per Share (the “Warrant Price”) all as set forth above and as adjusted pursuant to this Warrant, subject to the provisions and upon the terms
and conditions set forth in this Warrant. 
 ARTICLE 1 

 EXERCISE 

1.1      Method of Exercise.  Holder may exercise this Warrant by delivering this Warrant and a
duly executed Notice of Exercise in substantially the form attached as Appendix 1 to the principal office of the Company (or such other appropriate location as Holder is so instructed by the Company). Holder shall also deliver to the Company a
check, wire transfer (to an account designated by the Company) or other form of payment acceptable to the Company for the aggregate Warrant Price for the Shares being purchased. 

1.2      Delivery of Certificate and New Warrant.  Within 45 days after Holder exercises this
Warrant and delivers to the Company the aggregate Warrant Price for the Shares being purchased, the Company shall deliver to Holder certificates for the Shares acquired and, if this Warrant has not been fully exercised and has not expired, a new
warrant representing the Shares not so acquired. 
 1.3      Replacement of Warrants.  In the
case of loss, theft or destruction of this Warrant, on delivery of an indemnity agreement reasonably satisfactory in form and amount to the Company or, in the case of mutilation, on surrender and cancellation of this Warrant, the Company at its
expense shall execute and deliver, in lieu of this Warrant, a new warrant of like tenor. 

 1.4        Acquisition of the Company. 

1.4.1    “Acquisition.” For the purpose of this Warrant, “Acquisition” means (a) any
sale, license, or other disposition of all or substantially all of the assets (including intellectual property) of the Company, or (b) any reorganization, consolidation, merger, sale of the outstanding voting securities of the Company or other
transaction or series of related transactions where the holders of the Company’s securities before the transaction or series of related transactions beneficially own less than 50% of the outstanding voting securities of the surviving entity
after the transaction or series of related transactions. 
 1.4.2    “Cash Acquisition.” For the
purpose of this Warrant, “Cash Acquisition” means any Acquisition in which the consideration paid by the acquirer is comprised solely of cash, promissory notes and/or the assumption of indebtedness. 

1.4.3    Assumption of Warrant.  Upon the closing of any Acquisition (other than a Cash Acquisition),
and as a condition precedent thereto, the successor or surviving entity shall assume the obligations of this Warrant, and this Warrant shall be exercisable for the same securities, cash, and/or property as would be payable for the Shares issuable
upon exercise of the unexercised portion of this Warrant as if such Shares were outstanding on the record date for the Acquisition and subsequent closing. The Warrant Price shall be adjusted accordingly, and the Warrant Price and number and class of
Shares shall continue to be subject to adjustment from time to time in accordance with the provisions hereof. 
 ARTICLE 2 

ADJUSTMENTS TO THE SHARES 

2.1        Stock Dividends, Splits, Etc.  If the Company declares or pays a dividend
on the its common stock payable in common stock, or other securities, or subdivides the outstanding common stock into a greater amount of common stock, then upon exercise of this Warrant, for each Share acquired, Holder shall receive, without cost
to Holder, the total number and kind of securities to which Holder would have been entitled had Holder owned the Shares of record as of the date the dividend or subdivision occurred. 

2.2        Reclassification, Exchange or Substitution.  Upon any reclassification,
exchange, substitution, or other event that results in a change of the number and/or class of the securities issuable upon exercise or conversion of this Warrant, Holder shall be entitled to receive, upon exercise or conversion of this Warrant, the
number and kind of securities and property that Holder would have received for the Shares if this Warrant had been exercised immediately before such reclassification, exchange, substitution, or other event. Such an event shall include any automatic
conversion of the outstanding or issuable securities of the Company of the same class or series as the Shares to common stock pursuant to the terms of the Company’s Amended and Restated Certificate of Incorporation, as amended from time to time
(the “Certificate of Incorporation”) upon the closing of a registered public offering of the Company’s common stock or other circumstance as provided for in the Certificate of Incorporation. The Company or its successor shall promptly
issue to Holder a new warrant for such new securities or other property. The new warrant shall provide for adjustments which shall be as nearly equivalent as may be practicable to the adjustments provided for in this

  
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Article 2 including, without limitation, adjustments to the Warrant Price and to the number of securities or property issuable upon exercise of the new warrant. The provisions of this
Section 2.2 shall similarly apply to successive reclassifications, exchanges, substitutions, or other events. 

2.3      Adjustments for Combinations, Etc.  If the outstanding Shares are combined or
consolidated, by reclassification, reverse split or otherwise, into a lesser Number of Shares, the Warrant Price shall be proportionately increased and the Number of Shares issuable upon exercise hereof shall be proportionately decreased. If the
outstanding Shares are split or multiplied, by reclassification or otherwise, into a greater Number of Shares, the Warrant Price shall be proportionately decreased and the Number of Shares issuable upon exercise hereof shall be proportionately
increased. 
 2.4      Adjustments for Diluting Issuances.  The Number of Shares issuable
upon exercise of this Warrant shall be subject to adjustment, from time to time, in the manner set forth on Exhibit A in the event of Diluting Issuances (as defined on Exhibit A). 

2.5      No Impairment.  The Company shall not, by amendment of its Certificate of
Incorporation or through a reorganization, transfer of assets, consolidation, merger, dissolution, issue, or sale of securities or any other voluntary action, avoid or seek to avoid the observance or performance of any of the terms to be observed or
performed under this Warrant by the Company, but shall at all times in good faith assist in carrying out all the provisions of this Article 2 and in taking all such action as may be necessary or appropriate to protect Holder’s rights under
this Article 2 against impairment. Notwithstanding the foregoing, the Company shall not have been deemed to have impaired Holder’s rights hereunder if it amends its Certificate of Incorporation, or the holders of shares of the
Company’s Preferred Stock waive rights thereunder, in a manner that does not affect Holder in a manner different form the effect that such amendments or waivers have on the rights of all holders of the Series B Preferred Stock. 

2.6      Certificate as to Adjustments.  Upon each adjustment of the Warrant Price, the Company
at its expense shall promptly compute such adjustment, and furnish Holder with a certificate signed by its Chief Financial Officer or other authorized officer setting forth such adjustment and the facts upon which such adjustment is based. The
Company shall, upon written request, furnish Holder a certificate setting forth the Warrant Price in effect upon the date thereof and the series of adjustments leading to such Warrant Price. 

2.7      Fractional Shares.  No fractional Shares shall be issuable upon exercise of this
Warrant and the Number of Shares to be issued shall be rounded down to the nearest whole Share. If a fractional share interest arises upon any exercise of the Warrant, the Company shall eliminate such fractional share interest by paying Holder an
amount computed by multiplying the fractional interest by the fair market value, as determined by the Company’s Board of Directors, of a full Share. 

  
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 ARTICLE 3 

REPRESENTATIONS AND COVENANTS OF THE COMPANY 

3.1      Representations and Warranties.  The Company hereby represents and warrants to, and
agrees with, the Holder as follows: 
 3.1.1    The initial Warrant Price referenced on the first page of this Warrant
is equal to the price paid per share (on a post-split basis) in the Company’s most recent preferred stock financing. 

3.1.2    All Shares which may be issued upon the exercise of the purchase right represented by this Warrant, and all
securities, if any, issuable upon conversion of the Shares, shall, upon issuance, be duly authorized, validly issued, fully paid and nonassessable, and free of any liens and encumbrances except for restrictions on transfer provided for herein or
under applicable federal and state securities laws. 
 3.1.3    The Company’s capitalization table attached to
this Warrant as Exhibit C is true and complete as of the Issue Date. 
 3.2        Notice of
Certain Events.  If the Company proposes at any time (a) to declare any dividend or distribution upon its stock, whether in cash, property, stock, or other securities and whether or not a regular cash dividend; (b) to offer
for subscription pro rata to all of the holders of any class or series of its stock any additional shares of Series C Preferred Stock; (c) to effect any reclassification or recapitalization of stock; or (d) to merge or consolidate with or
into any other corporation, or sell, lease, exclusively license, or convey all or substantially all of its assets, or to liquidate, dissolve or wind up, then, in connection with each such event, the Company shall give Holder (1) no later than
the date such written notice is provided to the Company’s stockholders, if any, written notice of the date on which a record will be taken for such dividend, distribution, or subscription rights (and specifying the date on which the holders of
stock will be entitled thereto) or for determining rights to vote, if any, in respect of the matters referred to in (a) and (b) above; and (2) in the case of the matters referred to in (c) and (d) above no later than the
date such written notice is provided to the Company’s stockholders, written notice of the date when the same will take place (and specifying the date on which the holders of stock will be entitled to exchange their stock for securities or other
property deliverable upon the occurrence of such event). Upon request, the Company shall provide Holder with such information reasonably necessary for Holder to evaluate its rights as a holder of this Warrant or Warrant Shares in the case of matters
referred to (a), (b), (c) and (d) herein above. 
 3.3        Information
Rights.  So long as the Holder holds this Warrant and/or any of the Shares, the Company shall deliver to the Holder (a) promptly after mailing, copies of all communiques to the stockholders of the Company, (b) within one
hundred fifty (150) days after the end of each fiscal year of the Company, a copy of the annual audited financial statements of the Company delivered to the Company’s investors and certified by independent public accountants of recognized
standing and (c) within forty-five (45) days after the end of each of the first three quarters of each fiscal year, the Company’s quarterly, unaudited financial statements. The Company’s obligations under this Section shall
terminate upon the Company being subject to the periodic reporting requirements of the Securities Exchange Act of 1934, as amended. In addition, and without limiting the generality of the foregoing, so long as the Holder holds this

  
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Warrant and/or any of the Shares, the Company shall afford to the Holder the same access to information concerning the Company and its business and financial condition as would be afforded to a
holder of the class of Shares under applicable state law and/or any agreement with any holder of the class of Shares. 

3.4       Registration Under Securities Act of 1933, as amended.  The Company agrees that the
Shares or, if the Shares are convertible into common stock of the Company, such common stock, shall be subject to the registration rights set forth on Exhibit B. 

3.5       Market Stand-Off Agreement. 

3.5.1    Market Standoff Period; Agreement.  The Holder agrees, if so requested by the managing
underwriter in connection with the Company’s initial public offering of equity securities not to effect (except as part of such underwritten registration in accordance with the registration rights provided pursuant to Exhibit B or pursuant
to a transaction exempt from registration (other than under Rule 144 or Rule 145 of the Securities Act)) any sale, distribution, short sale, loan, grant of options for the purchase of, or otherwise dispose of, any shares of the capital
stock or other securities of the Company for such period as such managing underwriter requests, such period in no event to commence earlier than seven (7) days prior to, or to end more than 180 days after, the effective date of such
registration. In addition, the Holder agrees to execute and deliver to any managing underwriter (or, in the case of any offering that is not underwritten, an investment banker) in connection with such registration any lock-up letter requested of the
Holder and in form and substance reasonably satisfactory to the managing underwriter. The Holder further agrees that the Company may instruct its transfer agent to place stop transfer notations in its records to enforce the provisions of this
Section 3.5.1. The foregoing restrictions shall be conditioned on each officer, director of the Company and holder of one percent or more of the Company’s Common Stock or securities convertible or exchangeable for one percent or more of
its Common Stock (determined in all instances on a fully diluted basis) being bound by substantially the same restrictions as are set forth above. 

3.5.2    Transferees Bound.  By accepting this warrant, the Holder agrees that it will not transfer this
warrant and/or the Shares unless the transferee(s) of such Holder agrees in writing to be bound by all of the provisions of this Section 3.5. 

ARTICLE 4 
 INVESTMENT
REPRESENTATIONS AND COVENANTS OF HOLDER 
 With respect to the acquisition of this Warrant and any of the Shares, Holder hereby
represents and warrants to, and agrees with, the Company as follows: 
 4.1       Purchase Entirely for Own
Account.  This Warrant is issued to Holder in reliance upon Holder’s representation to the Company that this Warrant and the Shares will be acquired for investment for Holder’s, or its affiliate’s, own account, not as a
nominee or agent, and not with a view to the resale or distribution of any part thereof other than to an affiliate, and that Holder has no present intention of selling, granting any participation in, or otherwise distributing the same other than to
an affiliate. By executing this Warrant, Holder further represents that except as otherwise set forth herein, Holder does not have any contract, undertaking, agreement 

  
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or arrangement with any person, other than an affiliate, to sell, transfer or grant participations to such person or to any third person with respect to any of the Shares. 

4.2      Reliance upon Holder’s Representations.  Holder understands that this Warrant and
the Shares are not registered under the Securities Act of 1933, as amended from time to time (the “Act”) on the ground that the issuance of such securities is exempt from registration under the Act, and that the Company’s reliance on
such exemption is predicated on Holder’s representations set forth herein. 
 4.3      Accredited
Investor Status.  Holder represents to the Company that Holder is an Accredited Investor (as defined in the Act). 

4.4      Restricted Securities.  Holder understands that this Warrant and the Shares are
“restricted securities” under the federal securities laws inasmuch as they are being acquired from the Company in a transaction not involving a public offering and that under such federal securities laws and applicable regulations such
securities may be resold without registration under the Securities Act only in certain limited circumstances. 
 ARTICLE 5 

MISCELLANEOUS 

5.1      Term; Exercise Upon Expiration.  This Warrant is exercisable in whole or in part, at
any time and from time to time on or before the earlier of (i) the Expiration Date set forth above and (ii) the consummation of a Cash Acquisition. 

5.2      Legends.  This Warrant and the Shares (and the securities issuable, directly or
indirectly, upon conversion of the Shares, if any) shall be imprinted with a legend in substantially the following form: 
 THIS WARRANT AND
THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR ANY APPLICABLE STATE SECURITIES LAWS, AND, EXCEPT AND PURSUANT TO THE PROVISIONS OF ARTICLE 5 BELOW, MAY NOT BE OFFERED,
SOLD OR OTHERWISE TRANSFERRED WITHOUT AN EFFECTIVE REGISTRATION THEREOF UNDER THE ACT AND ANY APPLICABLE STATE SECURITIES LAWS, OR PURSUANT TO RULE 144 OR AN EXEMPTION FROM THE REGISTRATION REQUIREMENTS OF THE ACT AND ANY APPLICABLE STATE
SECURITIES LAWS. 
 5.3      Compliance with Securities Laws on Transfer.  This Warrant and
the Shares issuable upon exercise of this Warrant (and the securities issuable, directly or indirectly, upon conversion of the Shares, if any) may not be transferred or assigned in whole or in part without compliance with applicable federal and
state securities laws by the transferor and the transferee. The Company shall not require Comerica Bank (“Bank”) or a Bank Affiliate (as defined herein) to provide an opinion of counsel or investment representation letter if the transfer
is to Bank’s parent company, Comerica Incorporated (“Comerica”), or any other affiliate of Bank (“Bank Affiliate”). 

  
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 5.4      Transfer Procedure.  After receipt of the
executed Warrant, Bank will transfer all of this Warrant to Comerica Ventures Incorporated, a non-banking subsidiary of Comerica and a Bank Affiliate (“Ventures”). Subject to the provisions of Section 4.3, Holder may transfer all or
part of this Warrant or the Shares issuable upon exercise of this Warrant (or the securities issuable, directly or indirectly, upon conversion of the Shares, if any) by giving the Company notice of the portion of this Warrant being transferred
setting forth the name, address and taxpayer identification number of the transferee and surrendering this Warrant to the Company for reissuance to the transferee(s) (and Holder, if applicable); provided, however, that Holder
may transfer all or part of this Warrant to its affiliates, including, without limitation, Ventures, at any time without notice or the delivery of any other instrument to the Company, and such affiliate shall then be entitled to all the rights of
Holder under this Warrant and any related agreements, and, upon receiving notice of such transfer, the Company shall cooperate fully in ensuring that any stock issued upon exercise of this Warrant is issued in the name of the affiliate that
exercises this Warrant. The terms and conditions of this Warrant shall inure to the benefit of, and be binding upon, the Company and the holders hereof and their respective permitted successors and assigns. Unless the Company is filing financial
information with the SEC pursuant to the Securities Exchange Act of 1934, the Company shall have the right to refuse to transfer any portion of this Warrant to any person who directly competes with the Company. 

5.5      Notices.  All notices and other communications from the Company to the Holder, or vice
versa, shall be deemed delivered and effective when given personally or mailed by first-class registered or certified mail, postage prepaid, or sent via a nationally recognized overnight courier service, fee prepaid, or on the first business day
after transmission by facsimile, at such address or facsimile number as may have been furnished to the Company or the Holder, as the case may be, in writing by the Company or such Holder from time to time. Effective upon the receipt of executed
Warrant and initial transfer described in Section 5.4 above, all notices to the Holder shall be addressed as follows until the Company receives notice of a change of address in connection with a transfer or otherwise: 

Comerica Bank c/o Comerica Incorporated 

Attn:  Warrant Administrator 

1717 Main Street, 5th Floor, MC 6406 

Dallas, Texas 75201 
 Facsimile
No.  (214) 462-4459 
 All notices to the Company shall be addressed as follows: 

ATYR PHARMA, INC. 
 3565
General Atomics Court, Suite 103 
 San Diego, CA 92121 

Attn:  President 

  
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 With a copy (which shall not constitute notice) to: 

DLA Piper LLP (US) 
 4365
Executive Drive, Suite 1100 
 San Diego, CA 92121 

Attn:   Randy Socol, Esq. 

FAX:   (858) 638-5057 

5.6          Amendments.  This Warrant and any term hereof may be changed, waived,
discharged or terminated only by an instrument in writing signed by the party against which enforcement of such change, waiver, discharge or termination is sought. 

5.7         Attorneys’ Fees.  In the event of any dispute between the parties
concerning the terms and provisions of this Warrant, the party prevailing in such dispute shall be entitled to collect from the other party all costs incurred in such dispute, including reasonable attorneys’ fees. 

5.8         Governing Law.  This Warrant shall be governed by and construed in
accordance with the laws of the State of California, without giving effect to its principles regarding conflicts of law. 

5.9         Confidentiality.  The Company hereby agrees to keep the terms and
conditions of this Warrant confidential. Notwithstanding the foregoing confidentiality obligation, the Company may disclose information relating to this Warrant (a) as required by law, rule, regulation, court order or other legal authority,
provided that (i) the Company has given Holder at least ten (10) days’ notice of such required disclosure, and (ii) the Company only discloses information that is required, in the opinion of counsel reasonably satisfactory to
Holder, to be disclosed or (b) as part of a due diligence investigation and Company shall use commercially reasonable efforts in obtaining an agreement from the party receiving such information to be bound by a confidentiality provision. 

5.10      No Stockholder Rights.  This warrant in and of itself shall not entitle the Holder to
any voting rights or other rights as a stockholder of the Company. 
 5.11      California Corporate
Securities Law.  THIS WARRANT AND THE SALE OF THE SECURITIES THAT ARE THE SUBJECT OF THIS WARRANT HAVE NOT BEEN QUALIFIED WITH THE COMMISSIONER OF CORPORATIONS OF THE STATE OF CALIFORNIA AND THE ISSUANCE OF THE WARRANT AND SUCH
SECURITIES OR THE PAYMENT OR RECEIPT OF ANY PART OF THE CONSIDERATION THEREFORE PRIOR TO THE QUALIFICATION IS UNLAWFUL, UNLESS THE SALE OF SECURITIES IS EXEMPT FROM THE QUALIFICATION BY SECTIONS 25100, 25102, OR 25105 OF THE CALIFORNIA
CORPORATIONS CODE, THE RIGHTS OF ALL PARTIES TO THIS WARRANT ARE EXPRESSLY CONDITIONED UPON THE QUALIFICATION BEING OBTAINED, UNLESS THE SALE IS SO EXEMPT. 

  
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 IN WITNESS HEREOF, the undersigned parties have caused this Warrant to be executed as of
the date first set forth above. 
  

					
	ATYR PHARMA, INC.	 	
		
	By:	 	 /s/ Jeffrey D. Watkins

	Name:	 	Jeffrey D. Watkins, Ph.D.	 	
	Title:	 	President and Chief Executive Officer	 	

  

					
	AGREED AND ACKNOWLEDGED:
	
	COMERICA BANK
		
	By:	 	 /s/ Steven J. Stuckey

	Name:	 	Steven J. Stuckey
	Title:	 	SVP

  
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 APPENDIX 1 

NOTICE OF EXERCISE 

1.      The undersigned hereby elects to purchase
                shares of the                   stock of ATYR PHARMA, INC.
pursuant to the terms of the attached Warrant, and tenders herewith payment of the purchase price of such shares in full. 

2.      Please issue a certificate or certificates representing said shares in the name of the undersigned or in
such other name as is specified below: 
 Comerica Ventures Incorporated 

Attn:  Warrant Administrator 

1717 Main Street, 5th Floor, MC 6406 

Dallas, Texas  75201 

Facsimile No.  (214) 462-4459 

3.      The undersigned further acknowledges that it has reviewed the “Market Stand-Off” agreement set
forth in Section 3.5 of the Warrant and agrees to be bound by such provisions. 
 4.      The undersigned
hereby represents and warrants that the representations and warranties set forth in Article 4 of the Warrant are true and correct in all respects as of the date hereof with respect to the undersigned’s acquisition of the Shares. 

COMERICA VENTURES INCORPORATED or Assignee 

	
	
	  

	(Signature)
	
	  

	(Name and Title)
	
	  

	(Date)

 EXHIBIT A 

Anti-Dilution Provisions 
 (For
Preferred Stock Warrants With Existing Anti-Dilution Protection) 
 In the event of the issuance (a “Diluting Issuance”) by
the Company, after the Issue Date of this Warrant, of securities at a price per share less than the Warrant Price, then the number of shares of common stock issuable upon conversion of the Shares shall be adjusted in accordance with those provisions
(including any exceptions or exclusions to any adjustment) of the Company’s Certificate of Incorporation which apply to Diluting Issuances (the “Provisions”). 

 EXHIBIT B 

Registration Rights 
 The
common stock issuable upon conversion of the Shares, shall be deemed “registrable securities” entitled to “Incidental Registration” rights in accordance with the terms of the following agreement (the “Agreement”)
between the Company and its investor(s): 
 Third Amended and Restated Registration Rights Agreement made and entered into as of
October 6, 2010, as amended from time to time. 
 By acceptance of the Warrant to which this Exhibit B is attached, Holder shall
be deemed to be a party to the Agreement solely for the purpose of the above-mentioned registration rights. 

 EXHIBIT C 

Capitalization TableEX-4.4

 Exhibit 4.4 

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR
THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN SECTIONS 5.3 AND 5.4 BELOW, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR IN FORM AND SUBSTANCE SATISFACTORY TO THE
COMPANY, SUCH OFFER, SALE, PLEDGE OR OTHER TRANSFER IS EXEMPT FROM SUCH REGISTRATION. 
 WARRANT TO PURCHASE STOCK 

 

			
	Company:	  	ATYR PHARMA, INC.
	Number of Shares:	  	59,312, plus all Additional Shares which Holder is entitled to purchase pursuant to Section 1.7
	Type/Series of Stock:	  	Series D Preferred
	Warrant Price:	  	$2.529 per share
	Issue Date:	  	July 24, 2013
	Expiration Date:	  	July 24, 2023 See also Section 5.1(b).
	Credit Facility:	  	This Warrant to Purchase Stock (“Warrant”) is issued in connection with that certain First Amendment to Loan and Security Agreement of even date herewith between Silicon Valley Bank and the Company (the
Loan and Security Agreement by and between Silicon Valley Bank and the Company dated as of April 25, 2012, as amended, the “Loan Agreement”).

 THIS WARRANT CERTIFIES THAT, for good and valuable consideration, SILICON VALLEY BANK (together with any
successor or permitted assignee or transferee of this Warrant or of any shares issued upon exercise hereof, “Holder”) is entitled to purchase the number of fully paid and non-assessable shares (the
“Shares”) of the above-stated Type/Series of Stock (the “Class”) of the above-named company (the “Company”) at the above-stated Warrant Price, all as set forth above and as
adjusted pursuant to Section 2 of this Warrant, subject to the provisions and upon the terms and conditions set forth in this Warrant. Reference is made to Section 5.4 of this Warrant whereby Silicon Valley Bank shall transfer this Warrant
to its parent company, SVB Financial Group. 
 SECTION 1. EXERCISE. 

1.1 Method of Exercise. Holder may at any time and from time to time exercise this Warrant, in whole or in part, by delivering to the
Company the original of this Warrant together with a duly executed Notice of Exercise in substantially the form attached hereto as Appendix 1 and, unless Holder is exercising this Warrant pursuant to a cashless exercise set forth in
Section 1.2, a check, wire transfer of same-day funds (to an account designated by the Company), or other form of payment acceptable to the Company for the aggregate Warrant Price for the Shares being purchased. 

1.2 Cashless Exercise. On any exercise of this Warrant, in lieu of payment of the aggregate Warrant Price in the manner as specified in
Section 1.1 above, but otherwise in accordance with the requirements of Section 1.1, Holder may elect to receive Shares equal to the value of this Warrant, or portion hereof as to which this Warrant is being exercised. Thereupon, the
Company shall issue to the Holder such number of fully paid and non-assessable Shares as are computed using the following formula: 
  

	
	X = Y(A-B)/A

 where: 

  
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	X =	  	the number of Shares to be issued to the Holder;
		
	Y =	  	the number of Shares with respect to which this Warrant is being exercised (inclusive of the Shares surrendered to the Company in payment of the aggregate Warrant Price);
		
	A =	  	the Fair Market Value (as determined pursuant to Section 1.3 below) of one Share; and
		
	B =	  	the Warrant Price.

 1.3 Fair Market Value. If the Company’s common stock is then traded or quoted on a nationally
recognized securities exchange, inter-dealer quotation system or over-the-counter market (a “Trading Market”) and the Class is common stock, the fair market value of a Share shall be the closing price or last sale price of a
share of common stock reported for the Business Day immediately before the date on which Holder delivers this Warrant together with its Notice of Exercise to the Company. If the Company’s common stock is then traded in a Trading Market and the
Class is a series of the Company’s convertible preferred stock, the fair market value of a Share shall be the closing price or last sale price of a share of the Company’s common stock reported for the Business Day immediately before the
date on which Holder delivers this Warrant together with its Notice of Exercise to the Company multiplied by the number of shares of the Company’s common stock into which a Share is then convertible. If the Company’s common stock is not
traded in a Trading Market, the Board of Directors of the Company shall determine the fair market value of a Share in its reasonable good faith judgment. 

1.4 Delivery of Certificate and New Warrant. Within a reasonable time after Holder exercises this Warrant in the manner set forth in
Section 1.1 or 1.2 above, the Company shall deliver to Holder a certificate representing the Shares issued to Holder upon such exercise and, if this Warrant has not been fully exercised and has not expired, a new warrant of like tenor
representing the Shares not so acquired. 
 1.5 Replacement of Warrant. On receipt of evidence reasonably satisfactory to the Company
of the loss, theft, destruction or mutilation of this Warrant and, in the case of loss, theft or destruction, on delivery of an indemnity agreement reasonably satisfactory in form, substance and amount to the Company or, in the case of mutilation,
on surrender of this Warrant to the Company for cancellation, the Company shall, within a reasonable time, execute and deliver to Holder, in lieu of this Warrant, a new warrant of like tenor and amount. 

1.6 Treatment of Warrant Upon Acquisition of Company. 

(a) Acquisition. For the purpose of this Warrant, “Acquisition” means any transaction or series of related
transactions involving: (i) the sale, lease, exclusive license, or other disposition of all or substantially all of the assets of the Company (ii) any merger or consolidation of the Company into or with another person or entity (other than
a merger or consolidation effected exclusively to change the Company’s domicile), or any other corporate reorganization, in which the stockholders of the Company in their capacity as such immediately prior to such merger, consolidation or
reorganization, own less than a majority of the Company’s (or the surviving or successor entity’s) outstanding voting power immediately after such merger, consolidation or reorganization; or (iii) any sale or other transfer by the
stockholders of the Company of shares representing at least a majority of the Company’s then-total outstanding combined voting power. 

  
 2 

 (b) Treatment of Warrant at Acquisition. In the event of an Acquisition in which the
consideration to be received by the Company’s stockholders consists solely of cash, solely of Marketable Securities or a combination of cash and Marketable Securities (a “Cash/Public Acquisition”), either (i) Holder
shall exercise this Warrant pursuant to Section 1.1 and/or 1.2 and such exercise will be deemed effective immediately prior to and contingent upon the consummation of such Acquisition or (ii) if Holder elects not to exercise the Warrant,
this Warrant will expire immediately prior to the consummation of such Acquisition. 
 (c) The Company shall provide Holder with written
notice of its request relating to the Cash/Public Acquisition (together with such reasonable information as Holder may reasonably require regarding the treatment of this Warrant in connection with such contemplated Cash/Public Acquisition giving
rise to such notice), which is to be delivered to Holder not less than seven (7) Business Days prior to the closing of the proposed Cash/Public Acquisition. In the event the Company does not provide such notice, then if, immediately prior to
the Cash/Public Acquisition, the fair market value of one Share (or other security issuable upon the exercise hereof) as determined in accordance with Section 1.3 above would be greater than the Warrant Price in effect on such date, then this
Warrant shall automatically be deemed on and as of such date to be exercised pursuant to Section 1.2 above as to all Shares (or such other securities) for which it shall not previously have been exercised, and the Company shall promptly notify
the Holder of the number of Shares (or such other securities) issued upon such exercise to the Holder and Holder shall be deemed to have restated each of the representations and warranties in Section 4 of the Warrant as of the date thereof.

 (d) Upon the closing of any Acquisition other than a Cash/Public Acquisition defined above, the acquiring, surviving or successor entity
shall assume the obligations of this Warrant, and this Warrant shall thereafter be exercisable for the same securities and/or other property as would have been paid for the Shares issuable upon exercise of the unexercised portion of this Warrant as
if such Shares were outstanding on and as of the closing of such Acquisition, subject to further adjustment from time to time in accordance with the provisions of this Warrant. 

(e) As used in this Warrant, “Marketable Securities” means securities meeting all of the following requirements:
(i) the issuer thereof is then subject to the reporting requirements of Section 13 or Section 15(d) of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), and is then current in its filing of all
required reports and other information under the Act and the Exchange Act; (ii) the class and series of shares or other security of the issuer that would be received by Holder in connection with the Acquisition were Holder to exercise this
Warrant on or prior to the closing thereof is then traded in Trading Market, and (iii) following the closing of such Acquisition, Holder would not be restricted from publicly re-selling all of the issuer’s shares and/or other securities
that would be received by Holder in such Acquisition were Holder to exercise or convert this Warrant in full on or prior to the closing of such Acquisition, except to the extent that any such restriction (x) arises solely under federal or state
securities laws, rules or regulations, and (y) does not extend beyond six (6) months from the closing of such Acquisition. 
 1.7
Additional Shares. Upon the funding of the Supplemental Growth Capital Advance (as defined in the Loan Agreement) under the Supplemental Second Tranche (as defined in the Loan Agreement), the Company shall be deemed to have automatically
granted to Holder, in addition to the number of Shares which this Warrant can otherwise be exercised for by Holder, the right to purchase that number of additional Shares, rounded upward to the nearest whole number, equal to One Hundred Fifty
Thousand Dollars ($150,000) divided by the Warrant Price (such additional shares being called the “Additional Shares”). 

  
 3 

 SECTION 2. ADJUSTMENTS TO THE SHARES AND WARRANT PRICE. 

2.1 Stock Dividends, Splits, Etc. If the Company declares or pays a dividend or distribution on the outstanding shares of the Class
payable in common stock or other securities or property (other than cash), then upon exercise of this Warrant, for each Share acquired, Holder shall receive, without additional cost to Holder, the total number and kind of securities and property
which Holder would have received had Holder owned the Shares of record as of the date the dividend or distribution occurred. If the Company subdivides the outstanding shares of the Class by reclassification or otherwise into a greater number of
shares, the number of Shares purchasable hereunder shall be proportionately increased and the Warrant Price shall be proportionately decreased. If the outstanding shares of the Class are combined or consolidated, by reclassification or otherwise,
into a lesser number of shares, the Warrant Price shall be proportionately increased and the number of Shares shall be proportionately decreased. 

2.2 Reclassification, Exchange, Combinations or Substitution. Upon any event whereby all of the outstanding shares of the Class are
reclassified, exchanged, combined, substituted, or replaced for, into, with or by Company securities of a different class and/or series, then from and after the consummation of such event, this Warrant will be exercisable for the number, class and
series of Company securities that Holder would have received had the Shares been outstanding on and as of the consummation of such event, and subject to further adjustment thereafter from time to time in accordance with the provisions of this
Warrant. The provisions of this Section 2.2 shall similarly apply to successive reclassifications, exchanges, combinations substitutions, replacements or other similar events. 

2.3 Conversion of Preferred Stock. If the Class is a class and series of the Company’s convertible preferred stock, in the event
that all outstanding shares of the Class are converted, automatically or by action of the holders thereof, into common stock pursuant to the provisions of the Company’s Amended and Restated Certificate of Incorporation (as amended from time to
time, the “Certificate of Incorporation”), including, without limitation, in connection with the Company’s initial, underwritten public offering and sale of its common stock pursuant to an effective registration
statement under the Act (the “IPO”), then from and after the date on which all outstanding shares of the Class have been so converted, this Warrant shall be exercisable for such number of shares of common stock into which the
Shares would have been converted had the Shares been outstanding on the date of such conversion, and the Warrant Price shall equal the Warrant Price in effect as of immediately prior to such conversion divided by the number of shares of common stock
into which one Share would have been converted, all subject to further adjustment thereafter from time to time in accordance with the provisions of this Warrant. 

2.4 Adjustments for Diluting Issuances. Without duplication of any adjustment otherwise provided for in this Section 2, the number of
shares of common stock issuable upon conversion of the Shares shall be subject to anti-dilution adjustment from time to time in the manner set forth in the Certificate of Incorporation as if the Shares were issued and outstanding on and as of the
date of any such required adjustment. 
 2.5 No Fractional Share. No fractional Share shall be issuable upon exercise of this Warrant
and the number of Shares to be issued shall be rounded down to the nearest whole Share. If a fractional Share interest arises upon any exercise of the Warrant, the Company shall eliminate such fractional Share interest by paying Holder in cash the
amount computed by multiplying the fractional 

  
 4 

 
interest by (i) the fair market value (as determined in accordance with Section 1.3 above) of a full Share, less (ii) the then-effective Warrant Price. 

2.6 Notice/Certificate as to Adjustments. Upon each adjustment of the Warrant Price, Class and/or number of Shares, the Company, at the
Company’s expense, shall notify Holder in writing within a reasonable time setting forth the adjustments to the Warrant Price, Class and/or number of Shares and facts upon which such adjustment is based. The Company shall, upon written request
from Holder, furnish Holder with a certificate of its Chief Financial Officer, including computations of such adjustment and the Warrant Price, Class and number of Shares in effect upon the date of such adjustment. 

SECTION 3. REPRESENTATIONS AND COVENANTS OF THE COMPANY. 

3.1 Representations and Warranties. The Company represents and warrants to, and agrees with, the Holder as follows: 

(a) The initial Warrant Price referenced on the first page of this Warrant is not greater than the price per share at which shares of the
Class were last sold and issued prior to the Issue Date hereof in an arms-length transaction in which at least $500,000 of such shares were sold. 

(b) All Shares which may be issued upon the exercise of this Warrant, and all securities, if any, issuable upon conversion of the Shares,
shall, upon issuance, be duly authorized, validly issued, fully paid and non-assessable, and free of any liens and encumbrances except for restrictions on transfer provided for herein or under applicable federal and state securities laws. The
Company covenants that it shall at all times cause to be reserved and kept available out of its authorized and unissued capital stock such number of shares of the Class, common stock and other securities as will be sufficient to permit the exercise
in full of this Warrant and the conversion of the Shares into common stock or such other securities. 
 (c) The Company’s
capitalization table attached hereto as Schedule 1 is true and complete, in all material respects, as of the Issue Date. 
 3.2 Notice of
Certain Events. If the Company proposes at any time to: 
 (a) declare any dividend or distribution upon the outstanding shares of the
Class or common stock, whether in cash, property, stock, or other securities and whether or not a regular cash dividend; 
 (b) offer for
subscription or sale pro rata to the holders of the outstanding shares of the Class any additional shares of any class or series of the Company’s stock (other than pursuant to contractual pre-emptive rights); 

(c) effect any reclassification, exchange, combination, substitution, reorganization or recapitalization of the outstanding shares of the
Class; 
 (d) effect an Acquisition or to liquidate, dissolve or wind up; or 

(e) effect an IPO; 
 then, in connection with
each such event, the Company shall give Holder: 

  
 5 

 (1) at least seven (7) Business Days prior written notice of the date on
which a record will be taken for such dividend, distribution, or subscription rights (and specifying the date on which the holders of outstanding shares of the Class will be entitled thereto) or for determining rights to vote, if any, in respect of
the matters referred to in (a) and (b) above; 
 (2) in the case of the matters referred to in (c) and
(d) above at least seven (7) Business Days prior written notice of the date when the same will take place (and specifying the date on which the holders of outstanding shares of the Class will be entitled to exchange their shares for the
securities or other property deliverable upon the occurrence of such event); and 
 (3) with respect to the IPO, at least
seven (7) Business Days prior written notice of the date on which the Company proposes to file its registration statement in connection therewith. 

Reference is made to Section 1.6(c) whereby this Warrant will be deemed to be exercised pursuant to Section 1.2 hereof if the Company does not give
written notice to Holder of a Cash/Public Acquisition as required by the terms hereof. Company will also provide information requested by Holder that is reasonably necessary to enable Holder to comply with Holder’s accounting or reporting
requirements. 
 SECTION 4. REPRESENTATIONS AND WARRANTIES OF THE HOLDER. 

The Holder represents and warrants to the Company as follows: 

4.1 Purchase for Own Account. This Warrant and the securities to be acquired upon exercise of this Warrant by Holder are being acquired
for investment for Holder’s account, not as a nominee or agent, and not with a view to the public resale or distribution within the meaning of the Act. Holder also represents that it has not been formed for the specific purpose of acquiring
this Warrant or the Shares. 
 4.2 Disclosure of Information. Holder is aware of the Company’s business affairs and financial
condition and has received or has had full access to all the information it considers necessary or appropriate to make an informed investment decision with respect to the acquisition of this Warrant and its underlying securities. Holder further has
had an opportunity to ask questions and receive answers from the Company regarding the terms and conditions of the offering of this Warrant and its underlying securities and to obtain additional information (to the extent the Company possessed such
information or could acquire it without unreasonable effort or expense) necessary to verify any information furnished to Holder or to which Holder has access. 

4.3 Investment Experience. Holder understands that the purchase of this Warrant and its underlying securities involves substantial
risk. Holder has experience as an investor in securities of companies in the development stage and acknowledges that Holder can bear the economic risk of such Holder’s investment in this Warrant and its underlying securities and has such
knowledge and experience in financial or business matters that Holder is capable of evaluating the merits and risks of its investment in this Warrant and its underlying securities and/or has a preexisting personal or business relationship with the
Company and certain of its officers, directors or controlling persons of a nature and duration that enables Holder to be aware of the character, business acumen and financial circumstances of such persons. 

  
 6 

 4.4 Accredited Investor Status. Holder is an “accredited investor” within the
meaning of Regulation D promulgated under the Act. 
 4.5 The Act. Holder understands that this Warrant and the Shares issuable upon
exercise hereof (and the securities issuable, directly or indirectly, upon conversion of the Shares, if any) have not been registered under the Act in reliance upon a specific exemption therefrom, which exemption depends upon, among other things,
the bona fide nature of the Holder’s investment intent as expressed herein. Holder understands that this Warrant and the Shares issued upon any exercise hereof (and the securities issuable, directly or indirectly, upon conversion of the Shares,
if any) must be held indefinitely unless subsequently registered under the Act and qualified under applicable state securities laws, or unless exemption from such registration and qualification are otherwise available. Holder is aware of the
provisions of Rule 144 promulgated under the Act. 
 4.6 Market Stand-off Agreement. The Holder agrees that the Shares (and the
securities issuable, directly or indirectly, upon conversion of the Shares, if any) shall be subject to the holdback agreement in Section 4.2 of the Fourth Amended and Restated Registration Rights Agreement dated April 8, 2013, as amended
from time to time, by and among the Company and the investors party therein. 
 4.7 No Voting Rights. Holder, as a Holder of this
Warrant, will not have any voting rights until the exercise of this Warrant. 
 SECTION 5. MISCELLANEOUS. 

5.1 Term and Automatic Conversion Upon Expiration. 

(a) Term. Subject to the provisions of Section 1.6 above, this Warrant is exercisable in whole or in part at any time and from
time to time on or before 6:00 PM, Pacific time, on the Expiration Date and shall be void thereafter. 
 (b) Automatic Cashless Exercise
upon Expiration. In the event that, upon the Expiration Date, the fair market value of one Share (or other security issuable upon the exercise hereof) as determined in accordance with Section 1.3 above is greater than the Warrant Price in
effect on such date, then this Warrant shall automatically be deemed on and as of such date to be exercised pursuant to Section 1.2 above as to all Shares (or such other securities) for which it shall not previously have been exercised, and the
Company shall, within a reasonable time, deliver a certificate representing the Shares (or such other securities) issued upon such exercise to Holder. 

5.2 Legends. The Shares (and the securities issuable, directly or indirectly, upon conversion of the Shares, if any) shall be imprinted
with a legend in substantially the following form: 
 THE SHARES EVIDENCED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER THE SECURITIES
ACT OF 1933, AS AMENDED (THE “ACT”), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN THAT CERTAIN WARRANT TO PURCHASE STOCK ISSUED BY THE ISSUER TO SILICON VALLEY BANK DATED JULY 24, 2013, MAY NOT BE OFFERED,
SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR IN FORM AND SUBSTANCE SATISFACTORY TO THE 

  
 7 

 
ISSUER, SUCH OFFER, SALE, PLEDGE OR OTHER TRANSFER IS EXEMPT FROM SUCH REGISTRATION. 

5.3 Compliance with Securities Laws on Transfer. This Warrant and the Shares issuable upon exercise of this Warrant (and the securities
issuable, directly or indirectly, upon conversion of the Shares, if any) may not be transferred or assigned in whole or in part except in compliance with applicable federal and state securities laws by the transferor and the transferee (including,
without limitation, the delivery of investment representation letters and legal opinions reasonably satisfactory to the Company, as reasonably requested by the Company). The Company shall not require Holder to provide an opinion of counsel if the
transfer is to SVB Financial Group (Silicon Valley Bank’s parent company) or any other affiliate of Holder, provided that any such transferee is an “accredited investor” as defined in Regulation D promulgated under the Act.
Additionally, the Company shall also not require an opinion of counsel if there is no material question as to the availability of Rule 144 promulgated under the Act. 

5.4 Transfer Procedure. After receipt by Silicon Valley Bank of the executed Warrant, Silicon Valley Bank will transfer all of this
Warrant to its parent company, SVB Financial Group. By its acceptance of this Warrant, SVB Financial Group hereby makes to the Company each of the representations and warranties set forth in Section 4 hereof and agrees to be bound by all of the
terms and conditions of this Warrant as if the original Holder hereof. Subject to the provisions of Section 5.3 and upon providing the Company with written notice, SVB Financial Group and any subsequent Holder may transfer all or part of this
Warrant or the Shares issuable upon exercise of this Warrant (or the securities issuable directly or indirectly, upon conversion of the Shares, if any) to any transferee, provided, however, in connection with any such transfer, SVB Financial Group
or any subsequent Holder will give the Company notice of the portion of the Warrant being transferred with the name, address and taxpayer identification number of the transferee and Holder will surrender this Warrant to the Company for reissuance to
the transferee(s) (and Holder if applicable); and provided further, that any subsequent transferee other than SVB Financial Group shall agree in writing with the Company to be bound by all of the terms and conditions of this Warrant. Notwithstanding
any contrary provision herein, at all times prior to the IPO, Holder may not, without the Company’s prior written consent, transfer this Warrant or any portion hereof, or any Shares issued upon any exercise hereof, or any shares or other
securities issued upon any conversion of any Shares issued upon any exercise hereof, to any person or entity who directly competes with the Company, except in connection with an Acquisition of the Company by such a direct competitor. 

5.5 Notices. All notices and other communications hereunder from the Company to the Holder, or vice versa, shall be deemed delivered
and effective (i) when given personally, (ii) on the third (3rd) Business Day after being mailed by first-class registered or certified mail, postage prepaid, (iii) upon actual receipt if given by facsimile or electronic mail and
such receipt is confirmed in writing by the recipient, or (iv) on the first Business Day following delivery to a reliable overnight courier service, courier fee prepaid, in any case at such address as may have been furnished to the Company or
Holder, as the case may be, in writing by the Company or such Holder from time to time in accordance with the provisions of this Section 5.5. All notices to Holder shall be addressed as follows until the Company receives notice of a change of
address in connection with a transfer or otherwise: 
 SVB Financial Group 

Attn: Treasury Department 
 3003
Tasman Drive, HC 215 
 Santa Clara, CA 95054 

  
 8 

 Telephone: (408) 654-7400 

Facsimile: (408) 988-8317 

Email address: derivatives@svb.com 

Notice to the Company shall be addressed as follows until Holder receives notice of a change in address: 

aTyr Pharma, Inc. 
 Attn: Chief
Financial Officer 
 3545 John Hopkins Court, #250 

San Diego, CA 92121 
 Telephone:
(858) 731-8392 
 Facsimile: (858) 731-8394 

Email: sblackburn@atyrpharma.com 

5.6 Waiver. This Warrant and any term hereof may be changed, waived, discharged or terminated (either generally or in a particular
instance and either retroactively or prospectively) only by an instrument in writing signed by the party against which enforcement of such change, waiver, discharge or termination is sought. 

5.7 Attorney’s Fees. In the event of any dispute between the parties concerning the terms and provisions of this Warrant, the
party prevailing in such dispute shall be entitled to collect from the other party all costs incurred in such dispute, including reasonable attorneys’ fees. 

5.8 Counterparts; Facsimile/Electronic Signatures. This Warrant may be executed in counterparts, all of which together shall constitute
one and the same agreement. Any signature page delivered electronically or by facsimile shall be binding to the same extent as an original signature page with regards to any agreement subject to the terms hereof or any amendment thereto. 

5.9 Governing Law. This Warrant shall be governed by and construed in accordance with the laws of the State of California, without
giving effect to its principles regarding conflicts of law. 
 5.10 Headings. The headings in this Warrant are for purposes of
reference only and shall not limit or otherwise affect the meaning of any provision of this Warrant. 
 5.11 Business Days.
“Business Day” is any day that is not a Saturday, Sunday or a day on which Silicon Valley Bank is closed. 

[Remainder of page left blank intentionally] 

[Signature page follows] 

  
 9 

 IN WITNESS WHEREOF, the parties have caused this Warrant to Purchase Stock to be executed by
their duly authorized representatives effective as of the Issue Date written above. 
  

			
	“COMPANY”
	
	ATYR PHARMA, INC.
		
	By:	 	 /s/ JOHN MENDLEIN

		
	Name:	 	 JOHN MENDLEIN

		 	(Print)
		
	Title:	 	CEO
	
	“HOLDER”
	
	SILICON VALLEY BANK
		
	By:.	 	 /s/ KEVIN WALLACE

		
	Name:.	 	 KEVIN WALLACE

		 	(Print)
		
	Title:	 	VICE PRESIDENT

 APPENDIX 1 

NOTICE OF EXERCISE 
 1.
The undersigned Holder hereby exercises its right purchase              shares of the Common/Series             
Preferred [circle one] Stock of ATYR PHARMA, INC. (the “Company”) in accordance with the attached Warrant To Purchase Stock, and tenders payment of the aggregate Warrant Price for such shares as follows: 

 

			
	 ̈	  	check in the amount of $             payable to order of the Company enclosed herewith
		
	 ̈	  	Wire transfer of immediately available funds to the Company’s account
		
	 ̈	  	Cashless Exercise pursuant to Section 1.2 of the Warrant
		
	 ̈	  	Other [Describe]
                                         
                                         
          

 2. Please issue a certificate or certificates representing the Shares in the name specified below: 

 

			
	  
	 	
	 Holder’s Name
	 	
		
	  
	 	
		
	  
	 	
	 (Address)
	 	

 3. By its execution below and for the benefit of the Company, Holder hereby restates each of the
representations and warranties in Section 4 of the Warrant to Purchase Stock as of the date hereof. 
  

			
	HOLDER:
	  

		
	By:	 	  

		
	Name:	 	  

		
	Title:	 	  

		
	(Date):	 	  

  
 Appendix 1 

 SCHEDULE 1 

Company Capitalization Table 

See attached 
  

 
  

Schedule I

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