Exhibit 10.1

 

ATYR PHARMA, INC.

SECURITIES PURCHASE AGREEMENT

THIS SECURITIES PURCHASE AGREEMENT (the “Agreement”) is made as of the 10th day
of April, 2019, by and among aTyr Pharma, Inc., a Delaware corporation (the
“Company”), and the investors set forth on the signature pages hereto (the
“Investors” and each, an “Investor”).

WHEREAS, the Investors wish to purchase, and the Company wishes to sell, upon
the term and conditions stated in this Agreement, shares of the Company’s common
stock, par value $0.001 per share (the “Common Stock”), as described in this
Agreement, with the offer and sale of such shares to be made pursuant to the
Company’s Registration Statement and Prospectus (each as defined below);

NOW, THEREFORE, IN CONSIDERATION of the mutual covenants contained in this
Agreement, and for other good and valuable consideration, the receipt and
adequacy of which are hereby acknowledged, the Company and the Investors hereby
agree as follows:

1.

Purchase and Sale of the Shares.

1.1.Issue and Sale of Common Stock. Subject to the terms and conditions of this
Agreement, each Investor, severally and not jointly, agrees to purchase at the
Closing (as defined below), and the Company agrees to issue and sell to such
Investor at the Closing, the number of shares of the Company’s Common Stock set
forth on such Investor’s signature page hereto at a purchase price of $0.541 per
share.  The shares of Common Stock to be purchased at the Closing hereunder are
referred to herein as the “Shares”.

1.2.Closing. Upon satisfaction or waiver of the conditions set forth in Section
1.3, the purchase and sale of the Shares shall take place at the offices of
Goodwin Procter LLP located at 3 Embarcadero Center, Floor 28, San Francisco,
California at 10:00 A.M., on April 12, 2019, or at such other time and place as
the Company and the Investors may mutually agree upon in writing (which time and
place are designated as the “Closing”). At the Closing, the Company shall cause
its transfer agent to deliver to each Investor, via electronic book-entry,
registered in the name of each Investor or, if so indicated on the Investor
Questionnaire attached hereto as Exhibit A, in the name of a nominee designated
by such Investor, the Shares that such Investor is purchasing against payment of
the purchase price therefor by wire transfer of immediately available funds to
an account specified by the Company in writing to the Investors.

 

1.3.

Conditions.  

(a)The obligations of each Investor to purchase the Shares are subject to the
satisfaction or waiver by such Investor of the following conditions as of the
Closing:

(i)The accuracy in all material respects (or, to the extent representations or
warranties are qualified by materiality or Material Adverse Effect (as defined
below), in all respects) when made and as of the Closing of the representations
and warranties of the Company contained herein (unless as of a specific date
therein in which case they shall be accurate as of such date);

(ii)The Investors shall have received a certificate, dated the date of the
Closing, duly executed by an executive officer of the Company on behalf of the
Company, certifying that:

 

(A)

the condition specified in Section 1.3(a)(i) has been satisfied;

 

(B)

all obligations, covenants and agreements of the Company required to be
performed at or prior to the Closing have been performed;

(iii)The Investors shall have received a certificate, dated the date of the
Closing, duly executed by the secretary of the Company, certifying (A) the
Bylaws of the Company, and (B) resolutions of the Board approving this Agreement
and the transactions contemplated hereby;

(iv)The Investors shall have received, on or prior to the Closing, a copy of the
irrevocable instructions to the transfer agent instructing the transfer agent to
register the Shares in book entry form registered in the name of the Investor;

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(v)The Investors shall have received a copy of the Prospectus Supplement (as
defined below), which may be delivered in accordance with Rule 172 under the
Securities Act of 1933, as amended (the “Securities Act”);

(vi)The Company shall have received notification from the NASDAQ Capital Market
(“NASDAQ”) that the listing of additional shares review process has been
completed, and NASDAQ shall not have made any objection to consummation of the
transaction contemplated by this Agreement;

(vii)From the date hereof to the date of the Closing, trading in the Common
Stock shall not have been suspended by the Securities and Exchange Commission
(the “Commission”) or NASDAQ, and, at any time prior to the Closing, trading in
securities generally as reported by Bloomberg L.P. shall not have been suspended
or limited, or minimum prices shall not have been established on securities
whose trades are reported by such service, or on NASDAQ or any other trading
market or exchange, nor shall a banking moratorium have been declared either by
the United States or New York State authorities nor shall there have occurred
any material outbreak or escalation of hostilities or other national or
international calamity of such magnitude in its effect on, or any material
adverse change in, any financial market which, in each case, in the reasonable
judgment of such Investor, makes it impracticable or inadvisable to purchase the
Shares at the Closing; and

(viii)There shall have been no Material Adverse Effect (as defined in Section
2.1) with respect to the Company since the date hereof.

(b)The obligations of the Company to sell the Shares to the Investors are
subject to the satisfaction or waiver of the following condition as of the
Closing:

(i)The accuracy in all material respects (or, to the extent representations or
warranties are qualified by materiality or Material Adverse Effect, in all
respects) when made and as of the Closing of the representations and warranties
of the Investors contained herein (unless as of a specific date therein in which
case they shall be accurate as of such date); and

(ii)the Company shall have received notification from NASDAQ that the listing of
additional shares review process has been completed, and NASDAQ shall not have
made any objection to consummation of the transaction contemplated by this
Agreement.

2.

Representations, Warranties and Covenants of the Company. The Company hereby
represents and warrants to each Investor that:

2.1Organization and Qualification. The Company is a corporation duly
incorporated, validly existing and in good standing under the laws of the State
of Delaware, with the requisite power and authority to own and use its
properties and assets and to carry on its business as currently conducted. The
Company is not in violation or default of any of the provisions of its
certificate of incorporation, bylaws or other organizational or charter
documents. The Company is qualified to do business as a foreign entity and is in
good standing in each jurisdiction in which the nature of the business conducted
by the Company or its subsidiary makes such qualification necessary, except
where the failure to so qualify could not reasonably be expected to have a
Material Adverse Effect. For purposes of this Agreement, a “Material Adverse
Effect” means any material and adverse effect on (a) the assets, liabilities,
financial condition, business, or operations of the Company and its subsidiary,
taken as a whole or (b) the ability of the Company and its subsidiary, taken as
a whole, to carry out their business as of the date of this Agreement or to meet
their obligations under this Agreement on a timely basis.

2.2Authorization; Enforcement. The Company has the requisite corporate power and
authority to enter into and to consummate the transactions contemplated by this
Agreement and otherwise to carry out its obligations hereunder. The execution
and delivery of this Agreement by the Company and the consummation by it of the
transactions contemplated hereby have been duly authorized by the board of
directors of the Company and no further action is required by the Company, its
board of directors, or stockholders in connection therewith other than in
connection with the Required Approvals (as defined below). This Agreement has
been (or upon delivery will have been) duly executed by the Company and, when
delivered in accordance with the terms hereof, will constitute the

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valid and binding obligation of the Company enforceable against the Company in
accordance with its terms, except (a) as limited by general equitable principles
and applicable bankruptcy, insolvency, reorganization, moratorium and other laws
of general application affecting enforcement of creditors’ rights generally,
(b) as limited by laws relating to the availability of specific performance,
injunctive relief or other equitable remedies and (c) insofar as indemnification
and contribution provisions may be limited by applicable law (collectively, the
“Enforceability Exceptions”).

2.3No Conflicts. The execution, delivery and performance by the Company of this
Agreement, the issuance and sale of the Shares and the consummation by it of the
transactions contemplated hereby do not and will not (a) conflict with or
violate any provision of the Company’s certificate of incorporation, bylaws or
other organizational or charter documents; (b) conflict with, or constitute a
default (or an event that with notice or lapse of time or both would become a
default) under, result in the creation of any lien upon any of the properties or
assets of the Company or its subsidiary, or give to others any rights of
termination, amendment, anti-dilution or similar adjustments, acceleration or
cancellation (with or without notice, lapse of time or both) of, any agreement,
credit facility, debt or other instrument (evidencing a Company or subsidiary
debt or otherwise) or other understanding to which the Company or its subsidiary
is a party or by which any property or asset of the Company or its subsidiary is
bound or affected and which, in each case, is filed as an exhibit to the
Company’s Annual Report on Form 10-K for the year ended December 31, 2018 (the
“Annual Report”); or (c) subject to any Required Approvals, conflict with or
result in a violation of any law, rule, regulation, order, judgment, injunction,
decree or other restriction of any court or governmental authority to which the
Company is subject (including federal and state securities laws and
regulations), or by which any property or asset of the Company is bound or
affected, except in the case of each of clauses (b) and (c), such as would not
have or reasonably be expected to result in a Material Adverse Effect.

2.4Filings, Consents and Approvals. The Company is not required to obtain any
consent, waiver, authorization or order of, give any notice to, or make any
filing or registration with, any court or other federal, state, local or other
governmental authority or other person in connection with the execution,
delivery and performance by the Company of this Agreement, other than: (a) the
filing with the Commission of the Prospectus Supplement; (b) the notification to
NASDAQ for the listing of the Shares; and (c) such filings as are required to be
made under applicable state securities laws (collectively, the “Required
Approvals”).

2.5Issuance of Securities. The Shares have been duly authorized and, when issued
and paid for in accordance with this Agreement will be duly and validly issued,
fully paid and nonassessable.

2.6Registration. The Company meets the requirements for use of Form S-3 under
the Securities Act, and has filed with the Commission a registration statement
on such Form (Registration File No. 333-211998), which became effective as of
June 22, 2016, for the registration under the Securities Act of the Shares.  The
Company will file with the Commission pursuant to Rule 424(b) under the
Securities Act, and the rules and regulations (the “Rules and Regulations”) of
the Commission promulgated thereunder, a supplement to the form of prospectus
filed with the Commission on June 13, 2016 and related to such registration
statement, relating to the offer to sell and proposed sale of the Shares and the
plan of distribution thereof. Such registration statement, including the
exhibits thereto, as amended at the date of this Agreement, is hereinafter
called the “Registration Statement”; such prospectus in the form filed with the
Commission on June 13, 2016, is hereinafter called the “Base Prospectus”; the
supplemented form of prospectus, in the form in which it will be filed with the
Commission pursuant to Rule 424(b) is hereinafter called the “Prospectus
Supplement”; and the Base Prospectus and Prospectus Supplement are hereinafter
called the “Prospectus.” Any reference herein to the Registration Statement, the
Base Prospectus, the Prospectus Supplement or the Prospectus shall be deemed to
refer to and include the documents incorporated by reference therein (the
“Incorporated Documents”) pursuant to Item 12 of Form S-3 which were filed under
the Securities Exchange Act of 1934, as amended (the “Exchange Act”), on or
before the date of this Agreement, or the issue date of the Base Prospectus or
the Prospectus Supplement, as the case may be.  The sale of the Shares hereunder
meets the requirements of General Instruction I.B.6 of Form S-3. No stop order
suspending the effectiveness of the Registration Statement or any post-effective
amendment thereto has been issued under the Securities Act or Exchange Act, no
order preventing or suspending the use of the Base Prospectus or the Prospectus
Supplement has been issued and no proceedings for any of those purposes have
been instituted or are pending or, to the Company’s knowledge, contemplated. The
Company has complied with each request (if any) from the Commission for
additional information. Each of the Registration Statement and any
post-effective amendment thereto, at the time it became effective, complied in
all material respects with the Securities Act and the Exchange Act and the
applicable Rules and Regulations and did not

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and, as amended or supplemented, if applicable, will not, contain any untrue
statement of a material fact or omit to state a material fact required to be
stated therein or necessary to make the statements therein not misleading. Each
of the Base Prospectus and the Prospectus Supplement, as amended or
supplemented, does not contain any untrue statement of a material fact or omit
to state a material fact necessary in order to make the statements therein, in
light of the circumstances under which they were made, not misleading.
Notwithstanding the foregoing, the Company makes no representations or
warranties as to information, if any, contained in or omitted from the
Prospectus Supplement or any amendment thereof or supplement thereto in reliance
upon and in conformity with information furnished in writing to the Company by
or on behalf of any Investor specifically for use in the Prospectus Supplement.

2.7SEC Reports; Financial Statements.

(a)The Company has complied in all material respects with requirements to file
all reports, schedules, forms, statements and other documents required to be
filed by the Company under the Exchange Act, including pursuant to Section 13(a)
or 15(d) thereof, for the two years preceding the date hereof (or such shorter
period as the Company was required by law or regulation to file such material)
(the foregoing materials, including the exhibits thereto and documents
incorporated by reference therein, together with the Registration Statement and
the Prospectus being collectively referred to herein as the “SEC Reports”) The
financial statements of the Company included in the foregoing materials comply
in all material respects with applicable accounting requirements and the rules
and regulations of the Commission with respect thereto as in effect at the time
of filing. Such financial statements have been prepared in accordance with
United States generally accepted accounting principles applied on a consistent
basis during the periods involved (“GAAP”), except as may be otherwise specified
in such financial statements or the notes thereto and except that unaudited
financial statements may not contain all footnotes required by GAAP, and fairly
present in all material respects the financial position of the Company and its
consolidated subsidiaries as of and for the dates thereof and the results of
operations and cash flows for the periods then ended, subject, in the case of
unaudited statements, to normal, immaterial, year-end audit adjustments.

2.8Material Changes; Undisclosed Events, Liabilities or Developments. Since the
date of the latest audited financial statements included within the SEC Reports,
except as specifically disclosed in a subsequent SEC Report filed prior to the
date hereof, (a) there has been no event, occurrence or development that has had
or that would reasonably be expected to result in a Material Adverse Effect, (b)
the Company has not incurred any material liabilities (contingent or otherwise)
other than (i) trade payables and accrued expenses incurred in the ordinary
course of business consistent with past practice and (ii) liabilities not
required to be reflected in the Company’s financial statements pursuant to GAAP
or disclosed in filings made with the Commission, (c) the Company has not
altered its method of accounting, (d) the Company has not declared or made any
dividend or distribution of cash or other property to its stockholders or
purchased, redeemed or made any agreements to purchase or redeem any shares of
its capital stock and (e) the Company has not issued any equity securities to
any officer, director, or any person that, directly or indirectly through one or
more intermediaries, controls or is controlled by or is under common control
with a person as such terms are used in and construed under Rule 405 under the
Securities Act (an “Affiliate”), except pursuant to existing Company stock
option plans or except as contemplated by this Agreement.

2.9Litigation. Other than as disclosed in the Prospectus, there is no action,
suit, inquiry, notice of violation, proceeding or investigation pending or, to
the knowledge of the Company, threatened against or affecting the Company, its
subsidiary or any of their respective properties before or by any court,
arbitrator, governmental or administrative agency or regulatory authority
(federal, state, county, local or foreign) (collectively, an “Action”) which (a)
adversely affects or challenges the legality, validity or enforceability of any
of the Agreement, the Shares, or the transactions contemplated herein, or (b)
would, if there were an unfavorable decision, have or reasonably be expected to
result in a Material Adverse Effect. Neither the Company nor its subsidiary, nor
any director or officer thereof, is or has been the subject of any Action
involving a claim of violation of or liability under federal or state securities
laws or a claim of breach of fiduciary duty with respect to the Company or its
subsidiary. There has not been, and to the knowledge of the Company, there is
not pending or contemplated, any investigation by the Commission involving the
Company or any current or former director or officer of the Company in such
capacity. The Commission has not issued any stop order or other order suspending
the effectiveness of any registration statement filed by the Company or its
subsidiary under the Exchange Act or the Securities Act.

2.10  Compliance. Neither the Company nor its subsidiary: (a) is in default
under or in violation of (and no event has occurred that has not been waived
that, with notice or lapse of time or both, would result in a default by the

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Company or its subsidiary under), nor has the Company or its subsidiary received
notice of a claim that it is in default under or that it is in violation of, any
indenture, loan or credit agreement or any other agreement or instrument to
which it is a party or by which it or any of its properties is bound (whether or
not such default or violation has been waived) which, in each case, is filed as
an exhibit to the Annual Report; (b) is in violation of any judgment, decree or
order of any court, arbitrator or other governmental authority; or (c) is or has
been in violation of any statute, rule, ordinance or regulation of any
governmental authority, including without limitation all foreign, federal, state
and local laws relating to taxes, environmental protection, occupational health
and safety, product quality and safety and employment and labor matters, except
in each case as would not have or reasonably be expected to result in a Material
Adverse Effect

2.11  Listing. The Common Stock is registered pursuant to Section 12(b) or 12(g)
of the Exchange Act and is listed on NASDAQ under the symbol “LIFE”, and the
Company has taken no action designed to, or which to its knowledge is likely to
have the effect of, terminating the registration of the Common Stock under the
Exchange Act or de-listing the Shares from NASDAQ, nor has the Company received
any notification that the Commission or NASDAQ is contemplating terminating such
registration or listing, except as described in the Prospectus.

2.12  Capitalization. The capitalization of the Company is as set forth in the
SEC Reports.

2.13  Investment Company. The Company is not, and is not an Affiliate of, and
immediately after receipt of payment for the Shares, will not be or be an
Affiliate of, an “investment company” within the meaning of the Investment
Company Act of 1940, as amended. The Company shall conduct its business in a
manner so that it will not become an “investment company” subject to
registration under the Investment Company Act of 1940, as amended.

2.14  Registration Rights. Other than as disclosed in the SEC Reports, no person
has any right to cause the Company or its subsidiary to effect the registration
under the Securities Act of any securities of the Company.

2.15  Disclosure. Except with respect to the material terms and conditions of
the transactions contemplated by this Agreement, the Company confirms that
neither it nor any other person acting on its behalf has provided any of the
Investors or their agents or counsel with any information that it believes
constitutes or might constitute material, non-public information which is not
otherwise disclosed in the Prospectus Supplement or the SEC Reports. The Company
understands and confirms that the Investors will rely on the foregoing
representation in effecting transactions in securities of the Company. All of
the disclosure furnished by or on behalf of the Company to the Investors
regarding the Company and its subsidiary, their respective businesses and the
transactions contemplated hereby is true and correct in all material respects
and does not contain any untrue statement of a material fact or omit to state
any material fact necessary in order to make the statements made therein, in
light of the circumstances under which they were made, not misleading. The
Company acknowledges and agrees that no Investor makes or has made any
representations or warranties with respect to the transactions contemplated
hereby other than those specifically set forth in Section 3.

2.16 Acknowledgment Regarding Investors’ Purchase of Shares. The Company
acknowledges and agrees that each Investor is acting solely in the capacity of
an arm’s length purchaser with respect to this Agreement and the transactions
contemplated hereby. The Company further acknowledges that no Investor is acting
as a financial advisor or fiduciary of the Company (or in any similar capacity)
with respect to this Agreement and the transactions contemplated hereby and any
advice given by any Investor or any of their respective representatives or
agents in connection with this Agreement and the transactions contemplated
thereby is merely incidental to the Investor’s purchase of the Shares. The
Company further represents to each Investor that the Company’s decision to enter
into this Agreement has been based solely on the independent evaluation of the
transactions contemplated hereby by the Company and its representatives.

2.17   Maximum Investment. As of the Closing, the number of Shares issued to any
Investor (or any group of investors (as identified in a public filing made with
the Commission) of which the Investor is a party pursuant to this Agreement will
not constitute more than 17.5% of the issued and outstanding shares of Common
Stock (or securities convertible into or exercisable for shares of Common Stock)
or the voting power of the Company after giving effect to the issue and sale of
the Shares hereunder.

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3.

Representations and Warranties of the Investor. Each Investor hereby represents
and warrants to the Company that:

3.1Authorization; Enforcement. The Investor has full right, power and authority
to enter into this Agreement and to consummate the transactions contemplated
hereby and, if such Investor is not a natural person, has taken all necessary
action to authorize the execution, delivery and performance of this
Agreement.  This Agreement constitutes a valid and binding obligation of the
Investor enforceable against the Investor in accordance with its terms, except
as enforceability may be limited by the Enforceability Exceptions.

3.2No Conflicts. If the Investor is not a natural person, the execution,
delivery and performance by the Investor of this Agreement, the issuance and
sale of the Shares and the consummation by it of the transactions contemplated
hereby do not and will not conflict with or violate any provision of the
Investor’s certificate or articles of incorporation, bylaws or other
organizational or charter documents.

3.3Investor Questionnaire; Reliance. The Investor has answered all questions on
the signature page for use in preparation of the Prospectus Supplement and
Exhibit A hereto and the answers thereto are true and correct as of the date
hereof and will be true and correct as of the Closing, unless the Investor
otherwise notifies the Company in writing in accordance with Section 4.5 at
least one business day prior to Closing.  The Investor, in connection with its
decision to purchase the Shares, relied only upon the Base Prospectus, the
Prospectus Supplement, the Incorporated Documents, and any representations and
warranties of the Company contained herein.

3.4Access to Information. The Investor has had full access to the Base
Prospectus and the Incorporated Documents, and was able to read, review,
download and print such materials, if desired.  The Investor and its advisors,
if any, have been afforded the opportunity to ask questions of the Company.  The
Investor understands that its investment in the Shares involves a high degree of
risk, including the risks identified under the caption “Risk Factors” in the
Base Prospectus or Prospectus Supplement.  The Investor is knowledgeable,
sophisticated and experienced in making, and is qualified to make, decisions
with respect to investments in securities representing an investment decision
like that involved in the purchase of the Shares.  The Investor is able to bear
the economic risk of an investment in the Shares and, at the present time, is
able to afford a complete loss of such investment.

3.5State and Federal Review. The Investor understands that no United States
federal or state agency or any other government or governmental agency has
passed on or made any recommendation or endorsement of the Shares or the
fairness or suitability of the investment in the Shares nor have such
authorities passed upon or endorsed the merits of the offering of the Shares.

3.6Action outside the United States. The Investor acknowledges, represents and
agrees that no action has been or will be taken in any jurisdiction outside the
United States by the Company that would permit an offering of the Shares, or
possession or distribution of offering materials in connection with the issue of
the Shares in any jurisdiction outside the United States where action for that
purpose is required.

3.7Residency. The Investor, if a natural person, is a resident of that state or
country specified in its address on such Investor’s signature page hereof.

3.8Legal, Tax and Investment Advice. The Investor understands that nothing in
this Agreement or any other materials presented to the Investor in connection
with the purchase and sale of the Shares constitutes legal, tax or investment
advice. The Investor has consulted such legal, tax and investment advisors as
it, in its sole discretion, has deemed necessary or appropriate in connection
with its purchase of the Shares.

3.9Certain Transactions and Confidentiality. The Investor has not, directly or
indirectly, nor has any person acting on behalf of or pursuant to any
understanding with the Investor, executed any transactions in securities of the
Company, including short sales, prior to the date hereof.  The Investor has
maintained the confidentiality of all disclosures made to it in connection with
this transaction (including the existence and terms of this transaction).

3.10  Certain Representations.  The Investor acknowledges and agrees that the
Company makes or has made no representations or warranties with respect to the
transactions contemplated hereby other than those specifically set forth in
Section 2.

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4.

Miscellaneous.

4.1Successors and Assigns. Except as otherwise provided herein, the terms and
conditions of this Agreement shall inure to the benefit of and be binding upon
the respective successors and assigns of the parties. Nothing in this Agreement,
express or implied, is intended to confer upon any party other than the parties
hereto or their respective successors and assigns any rights, remedies,
obligations, or liabilities under or by reason of this Agreement, except as
expressly provided in this Agreement. The Company may not assign this Agreement
or any rights or obligations hereunder without the prior written consent of each
Investor (other than by merger).

4.2Governing Law. All questions concerning the construction, validity,
enforcement and interpretation of this Agreement shall be governed by and
construed and enforced in accordance with the internal laws of the State of New
York. Each party agrees that all legal proceedings concerning the
interpretations, enforcement and defense of the transactions contemplated by
this Agreement (whether brought against a party hereto or its respective
affiliates, directors, officers, shareholders, employees or agents) shall be
commenced exclusively in the state and federal courts sitting in the City of New
York. Each party hereby irrevocably submits to the exclusive jurisdiction of the
state and federal courts sitting in the City of New York, borough of Manhattan
for the adjudication of any dispute hereunder or in connection herewith or with
any transaction contemplated hereby or discussed herein, and hereby irrevocably
waives, and agrees not to assert in any suit, action or proceeding, any claim
that it is not personally subject to the jurisdiction of any such court, that
such suit, action or proceeding is improper or is an inconvenient venue for such
proceeding.

4.3Counterparts; Facsimile or Electronic Transmission. This Agreement may be
executed in two or more counterparts, each of which shall be deemed an original,
but all of which together shall constitute one and the same instrument.
Facsimile (provided confirmation of transmission is mechanically or
electronically generated and kept on file by the sending party) or electronic
transmission signatures shall be as effective as original signatures.

4.4Titles and Subtitles. The titles and subtitles used in this Agreement are
used for convenience only and are not to be considered in construing or
interpreting this Agreement.

4.5Notices. Any notices, consents, waivers or other communications required or
permitted to be given under the terms of this Agreement must be in writing and
will be deemed to have been delivered:  (i) upon receipt, when delivered
personally; (ii) when sent by facsimile (provided confirmation of transmission
is mechanically or electronically generated and kept on file by the sending
party); or (iii) one business day after deposit with a nationally recognized
overnight delivery service, in each case properly addressed to the party to
receive the same.  The addresses and facsimile numbers for such communications
shall be the address and number indicated for such party on the signature page
hereof.

4.6Finder’s Fee. Each party represents that it neither is nor will be obligated
for any finders’ fee or commission in connection with this transaction. Each
Investor agrees to indemnify and to hold harmless the Company from any liability
for any commission or compensation in the nature of a finders’ fee (and the
costs and expenses of defending against such liability or asserted liability)
for which such Investor or any of its officers, partners, employees, or
representatives is responsible. The Company agrees to indemnify and hold
harmless each Investor from any liability for any commission or compensation in
the nature of a finders’ fee (and the costs and expenses of defending against
such liability or asserted liability) for which the Company or any of its
officers, employees or representatives is responsible.

4.7Indemnification of Federated Kaufmann. Subject to the provisions of this
Section 4.7, the Company will indemnify and hold The Federated Kaufmann Small
Cap Fund (“Federated Kaufmann”) and its directors, officers, stockholders,
members, partners, employees and agents (and any other persons with a
functionally equivalent role of a person holding such titles notwithstanding a
lack of such title or any other title), each person who controls Federated
Kaufmann (within the meaning of Section 15 of the Securities Act and Section 20
of the Exchange Act), and the directors, officers, shareholders, agents,
members, partners or employees (and any other persons with a functionally
equivalent role of a person holding such titles notwithstanding a lack of such
title or any other title) of such controlling persons (each, an “Investor
Party”) harmless from any and all losses, liabilities, obligations, claims,
contingencies, damages, costs and expenses, including all judgments, amounts
paid in settlements, court costs and reasonable attorneys’ fees and costs of
investigation that any such Investor Party may suffer or incur as a result of or
relating to

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(a) any breach of any of the representations, warranties, covenants or
agreements made by the Company in this Agreement or (b) any action instituted
against the Investor Parties in any capacity, or any of them or their respective
Affiliates, by any stockholder of the Company who is not an Affiliate of such
Investor Party, with respect to any of the transactions contemplated by this
Agreement (unless such action is based upon a breach of such Investor Party’s
representations, warranties or covenants under this Agreement or any agreements
or understandings such Investor Party may have with any such stockholder or any
violations by such Investor Party of state or federal securities laws or any
conduct by such Investor Party which constitutes fraud, gross negligence,
willful misconduct or malfeasance). If any action shall be brought against any
Investor Party in respect of which indemnity may be sought pursuant to this
Agreement, such Investor Party shall promptly notify the Company in writing, and
the Company shall have the right to assume the defense thereof with counsel of
its own choosing reasonably acceptable to the Investor Party. Any Investor Party
shall have the right to employ separate counsel in any such action and
participate in the defense thereof, but the fees and expenses of such counsel
shall be at the expense of such Investor Party except to the extent that (i) the
employment thereof has been specifically authorized by the Company in writing,
(ii) the Company has failed after a reasonable period of time to assume such
defense and to employ counsel or (iii) in such action there is, in the
reasonable opinion of counsel, a material conflict on any material issue between
the position of the Company and the position of such Investor Party, in which
case the Company shall be responsible for the reasonable fees and expenses of no
more than one such separate counsel. The Company will not be liable to any
Investor Party under this Agreement (y) for any settlement by an Investor Party
effected without the Company’s prior written consent, which shall not be
unreasonably withheld or delayed; or (z) to the extent, but only to the extent
that a loss, claim, damage or liability is attributable to any Investor Party’s
breach of any of the representations, warranties, covenants or agreements made
by such Investor Party in this Agreement. The indemnification required by this
Section 4.7 shall be made by periodic payments of the amount thereof during the
course of the investigation or defense, as and when bills are received or are
incurred. The indemnity agreements contained herein shall be in addition to any
cause of action or similar right of any Investor Party against the Company or
others and any liabilities the Company may be subject to pursuant to law.

4.8Equal Treatment of Investors. No consideration (including any modification of
this Agreement) shall be offered or paid to any person to amend or consent to a
waiver or modification of any provision of this Agreement unless the same
consideration is also offered to all of the parties to the Agreement. For
clarification purposes, this provision constitutes a separate right granted to
each Investor by the Company and negotiated separately by each Investor, and is
intended for the Company to treat the Investors as a class and shall not in any
way be construed as the Investors acting in concert or as a group with respect
to the purchase, disposition or voting of the Shares or otherwise.

4.9Amendments and Waivers. Any term of this Agreement may be amended and the
observance of any term of this Agreement may be waived (either generally or in a
particular instance and either retroactively or prospectively), only with the
written consent of the Company and each Investor.

4.10  Severability. If one or more provisions of this Agreement are held to be
unenforceable under applicable law, such provision shall be excluded from this
Agreement and the balance of the Agreement shall be interpreted as if such
provision were so excluded and shall be enforceable in accordance with its
terms.

4.11  Entire Agreement. This Agreement and the other documents referred to
herein constitute the entire agreement among the parties and no party shall be
liable or bound to any other party in any manner by any warranties,
representations, or covenants except as specifically set forth herein or
therein.

[Signature Pages Follow]

 

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IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the
day and year first above written.

aTyr Pharma, Inc.

 

 

 

 

By:

 

/s/ Jill M. Broadfoot

Name:

 

Jill M. Broadfoot

Title:

 

 Chief Financial Officer

 

 

 

 

Address:

  

3545 John Hopkins Court, Suite #250

 

  

San Diego, California 92121

[Investor Signature Pages Follow]

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[INVESTOR SIGNATURE PAGES TO SECURITIES PURCHASE AGREEMENT]

IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the
day and year first above written.

Name of Investor: Schimmel Revocable Trust Cleo Schimmel Ttee Paul R. Schimmel
Ttee. U/ A Dtd 09/06/2000

Signature of Authorized Signatory of Investor:   /s/ Paul
Schimmel                                       
                                       

Name of Authorized Signatory:    Paul
Schimmel                                      
                                                                   

Title of Authorized Signatory:       Trustee                                   
                                                                                

Email Address of Authorized Signatory:                                          
                                                                            

Facsimile Number of Authorized Signatory:
                                         
                                                                      

Address for Notice of Investor:  

 

 

 

Number of Shares of Common Stock to Be Purchased:
       1,828,428                               

Total Purchase Price: $ 999,999.55      

 

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[INVESTOR SIGNATURE PAGES TO SECURITIES PURCHASE AGREEMENT]

IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the
day and year first above written.

Name of Investor: Federated Kaufman Small Cap Fund

Signature of Authorized Signatory of Investor:   /s/ Thomas M.
Brakel                                                                         
 

Name of Authorized Signatory:    Thomas M.
Brakel                                      
                                                               

Title of Authorized Signatory:       Portfolio
Manager                                   
                                                                  

Email Address of Authorized Signatory:                                          
                                                                            

Facsimile Number of Authorized Signatory:
                                         
                                                                      

Address for Notice of Investor:  

 

 

 

Number of Shares of Common Stock to Be Purchased:
       7,393,715                               

Total Purchase Price: $ 3,999,999.82      

 

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