SecProbe.io

January 20, 2015

Via E -mail
John D. Mendlein, Ph.D.
Chief Executive Officer and Executive Chairman
aTyr Pharma, Inc.
3545 John Hopkins Court, Suite #250
San Diego, CA 92121

Re: aTyr Pharma, Inc.
Draft Registration Statement on Form S -1
Submitted December 22, 2014
  CIK No. 0001339970

Dear Dr. Mendlein :

We have reviewed your draft registration statement  and have the following comments.  In
some of our comments, we may ask you to provide us with information so we may better
understand your disclosure.

Please respond to this letter by providing the requested information and either submitting
an amended draft registration statement or  publicly  filing your registration statement on
EDGAR.  If you do not believe our comments apply to your facts  and circumstances or do not
believe an amendment is appropriate, please tell us why in your response.

After reviewing the information you provide in response to these  comments  and your
amended draft registration statement or filed registration statemen t, we may have  additional
comments.

Prospectus Summary, page 1

1. Please revise the table on pages pages  2 and 80 to reflect only the current stage of
development for each product candidate and indication. Accordingly, please eliminate
columns for anticipated next milestone due to the uncertainty of such events.  Anticipated
milestone and other future events  are properly discussed in the text where they can be
placed in an appropriate context.

2. Please revise your pipeline table under the column labeled “Pathway” and in the text
included within the arrows to identify the applicable pathway, drug candidate, and
indication.  Alternatively, if you have not yet identified an indication for the arrow
labeled “Resolaris 4th Indication” or a drug candidate for the arrow labeled “iModFc non -
RMIC” or “Liver,” or a pathway for the arrow labeled “Lung,” please eliminate t hese
programs from the pipeline table on pages 2 and 80.

John D. Mendlein, Ph.D.
aTyr Pharma, Inc.
January 20, 2015
Page 2

Risks Associated with Our Business, page 4

3. We note your risk factor disclosure that the FDA has placed a full clinical hold on your
IND to evaluate Resolaris for adult patients with FSHD and that t his hold prohibits you
from continuing clinical trials of Resolaris in the United States.    In the sections of your
prospectus summary and business section where you discuss the expected timing of your
receipt of initial results for your Phase 1b/2 trial o f Resolaris, please expand your
disclosure to discuss the clinical hold, the specific issues highlighted by the FDA, any
material actions that you have taken or plan to take in response to the FDA’s
communications, any updates from the FDA with respect you r response to the clinical
hold, and how the clinical hold impacts your planned development of Resolaris for adult
patients with FSHD.

Risk Factors
We face potential product liability, and, if succe ssful claims are brought …, page 43

4. Please quantify the amount of product liability insurance you carry and whether the
amount of your coverage is typical for a company in your industry.

Use of Proceeds, page 53

5. Please disclose how far in the clinical development of Resolaris you expect the proceeds
from this  offering will enable you to proceed  by indication .  In this regard, we note that
your development of Resolaris in Adults with FSHD is your most advanced product
candidate.  You should disclose whether you expect the applicable proceeds will be
sufficient to fully fund each planned clinical trial or state what aspects of such trials you
will be able to accomplish using the applicable proceeds.

Management’s Discussion and Analysis of Financial Condition and Results of Operations
Stock -Based Compensation, pa ge 66

6. We may have additional comments on your accounting for equity issuances including
stock compensation and beneficial conversion features. Once you have an estimated
offering price, please provide us an analysis explaining the reasons for the differences
between recent valuations of your common stock leading up to the IPO and the estimated
offering price.

Business, page 77

7. Please provide a brief summary for each drug candidate included on your pipeline table
on pages 2 and 80.  For example, w e note that you have not provided a discussion of the
“discoveries” labeled Resolaris 4th Indication, Liver, or Lung.

John D. Mendlein, Ph.D.
aTyr Pharma, Inc.
January 20, 2015
Page 3

 8. Please discuss your plans to apply for orphan designation for Resolaris for any applicable
indications in the U.S. or European Union.

9. Please discuss the terms of Pangu BioPharma’s joint research agreement with HKUST R
and D Corporation Limited.  Please include all of the material terms agreed to by the
parties. This includes, but is not limited to:
 the material services provided;
 paymen t terms;
 the duration of the agreement; and
 the material termination provisions.

Phase 1b/2 Clinical Trial, page 93

10. We note on page 12 that your Phase 1b/2 trial of Resolaris is designed to show efficacy.
Please expand your disclosure to include the tr ials primary and secondary endpoints for
the trial in adult patients with FSHD.

Our Advisors , page 1 14

11. Please briefly discuss the function of your scientific advisory board and therapeutic
advisory board as well as the specific responsibilities of the advisory board members  and
the frequency of advisory board meetings.

Executive and Director Compensation, page 124

12. Please update your executive and director compensation disclosure to reflect
compensation information as of the registrant’s last completed fiscal year ended
December 31, 2014.  You should also continue to include 2013 executive compensation
information in your Summary Compensation Table.  Please refer to Instruction 1 to Item
402(n) of Regulation S -K.

Principal Stockholders, page 134

13. Please  update your table on page 134 as of the most recent practicable date.

Description of Capital Stock
Warrants, page 139

14. We note that you entered into a loan and security agreement with Comerica Bank in
September 2007.  Please expand your disclosure to cla rify whether this agreement has
terminated.  If this agreement is outstanding, please expand your disclosure to discuss the
material terms of this loan and security agreement.  Additionally, please file this
agreement as an exhibit pursuant to Item 601(b)( 10) of Regulation S -K. Alternatively,

John D. Mendlein, Ph.D.
aTyr Pharma, Inc.
January 20, 2015
Page 4

 please provide us with an analysis supporting your determination that this agreement is
not material to the company.

Shares Eligible for Future Sale, page 143

15. Please state the number of shares of common stock, upon c ompletion of this offering that
will be restricted securities under Rule 144.

16. Please state the number of shares that are subject to a lock -up.

Notes to Consolidated Financial Statements
Preferred Stock Warrant Liabilities, page F -10

17. You disclose that y ou will carry the warrants to purchase various shares of redeemable
convertible preferred stock as liabilities until such time as the warrant are no longer
outstanding or the underlying securities are no longer redeemable outside your control,
including th e completion of your IPO.  On page 139 you disclose that the various
warrants contain provisions for the adjustment of the warrant exercise price and number
of shares issuable for certain dilutive issuances.  Please explain to us how the exercise
terms of these warrants can be adjusted after the completion of your IPO and why these
provisions do not also trigger liability accounting.  In your response, please tell us
specifically whether the provision in Article IV Section B.4(c) of your existing
Certificat e of Incorporation will carry over in your post -IPO Certificate and, if so, how
this provision complies with the guidance in ASC 815 -40-55-42 and 55 -43.  In this
regard, it appears that the formula provided in this section adjusts for any issuance below
the previous exercise price of the warrants and is not limited to the dilutive effect of
future issuances below the then -current fair value.

Exhibit

18. Please file the join research agreement between Pangu BioPharma and HKUST R and D
Corporation Limited  as exhibit s pursuant to Item 601(b)(10) of Regulation S -K.
Alternatively, please provide us with an analysis supporting your determination that the
agreement is not material to the company.

Other Comments

19. Please file all exhibits as soon as practicable.  We may have further comments  upon
examination of these exhibits.

20. Prior to its use please provide us proofs of all graphic, visual or photographic  information
you will provide in the printed prospectus. Please note that we may  have comments
regarding this  material.

John D. Mendlein, Ph.D.
aTyr Pharma, Inc.
January 20, 2015
Page 5

 21. Please supplementally provide us with copies of all written communications, as defined
in Rule 405 under the Securities Act, that you, or anyone authorized to do so on your
behalf, present to potential investors in reliance on Section 5(d) of t he Securities Act,
whether or not they retain  copies of the communications.

You may contact Mark Brunhofer at (202) 551 -3638 if you have questions regarding
comments on the financial statements and related matters.  Please contact Matthew Jones at
(202) 5 51-3786, Bryan Pitko at (202) 551 -3203 or me at (202) 551 -3715 with any other
questions.

Sincerely,

 /s/ Bryan J. Pitko  for

Jeffrey P. Riedler
Assistant Director

cc:  Kingsley L. Taft
Maggie L. Wong
Mitzi Chang
Goodwin Procter LLP
3 Embarcadero Center, 24th Floor
San Francisco, CA 94111