EX-10.4



 Exhibit 10.4 
  





 
 December 20, 2013 

Mr. Frederic Chereau 
 [***] 

Dear Fred, 
 This letter is a formal offer
setting forth the principal terms for you to join aTyr Pharma, Inc. (the “Company”), a Delaware corporation, which is located in San Diego, California. This offer is contingent upon satisfactory completion of a background check. 

 

			
	 Position:
		 President and Chief Operating Officer

		
	 Location:
		 San Diego, CA

		
	 Status:
		 Full-Time, Exempt. This means you are paid for the job and not by the hour. Accordingly, you will not receive overtime pay if you work more than 8 hours in a
work day or 40 hours in a workweek.

		
	 Reporting to:
		 John Mendlein, Ph.D., Executive Chairman and Chief Executive Officer

		
	 Base Salary Rate:
		 $15,000.00 semi-monthly (which equals $360,000.00 per year) less applicable withholdings, paid in accordance with Company’s normal payroll practices.
Future adjustments in compensation, if any, will be made by the Company in its sole and absolute discretion.

		
	 Target Bonus:
		 Your annual target bonus will be 40% of your base salary with a range of 0-50% based upon the achievement of your individual goals, the achievement of team
goals and the achievement of corporate goals. Your annual target bonus is subject to review and approval by the aTyr Board of Directors. Any bonus would be prorated based upon service in the year.

		
	 Equity:
		 Shortly after commencement of your employment with the Company, and subject to approval by the board of directors, you will be granted an Option to purchase
1,987,795 shares of the Common Stock of the Company pursuant to the 2007 Stock Plan. The exercise price per share of the Option shall be the fair market value of the Common Stock, as determined by the board of directors at the time of the Option
grant. The specific terms and conditions of your Option will be subject to the terms



  
 



 









 



 
 Mr. Frederic Chereau 

December 20, 2013 
 Page two 

 


			
		  	 of the 2007 Stock Plan, as well as the terms set forth in a Stock Option Agreement between you and the Company. This Stock Option Agreement will be entered into
and executed after you commence your employment with the Company. In addition to the foregoing, in connection with the Company option grant, we anticipate that you will also be granted options to purchase a corresponding type and number of shares in
each of the entities which the Company has previously spun-out as stand-alone entities (the “Related Entities”). The specific terms and conditions of your options in the Related Entities will be subject to the terms of the 2012 Stock Plan
for each Related Entity, as well as the terms set forth in a Stock Option Agreement between you and the Related Entity.

		
	 Relocation Assistance:
	  	 You will be offered a lump sum relocation assistance payment in the amount of $45,000.00 to be paid at the time of your first paycheck. This amount will be
grossed up for tax purposes. This payment will be subject to repayment to the Company if you voluntarily resign within one year of commencing your employment. We will also reimburse you up to $6,000.00 per month for up to 6 months for temporary
housing.

		
	 Benefits:
	  	 You will be entitled to receive standard medical, life and dental insurance benefits for yourself and your dependents in accordance with Company policy. Company
reserves the right to change or eliminate these benefits on a prospective basis at any time.

		
	 401(k) Plan:
	  	 You will be eligible to participate in the aTyr Pharma, Inc. 401(k) Savings Plan immediately following the start of your employment.

		
	 Vacation &
 Sick
Time:
	  	 You will be entitled to accrue 15 days of vacation per year. You will have 6 days of sick time available each year.

		
	 Holidays:
	  	 You will be eligible for aTyr’s paid holidays. The schedule is published prior to the beginning of each calendar
year.



  
 



 









 



 
 Mr. Frederic Chereau 

December 20, 2013 
 Page three 

 


			
		
	 Employment at Will:
	  	 Your employment will be at-will, which means it may be terminated at any time by you or the Company with or without cause and that your employment is not for
any specific period of time. Any change to the at-will employment relationship must be by a specific, written agreement signed by you and the Company’s Chief Executive Officer.

		
	 Start Date:
	  	 January 9, 2014 based on a mutually agreed prorated part-time basis through February 28, 2014 or other mutually agreed full time status start
date.


 As a condition of your employment, you will be required to sign and abide by our Employee Nondisclosure and
Assignment Agreement when you begin your employment. A copy is attached for your reference. In addition, in order to comply with the Immigration Reform and Control Act of 1986, within three (3) days of your Start Date you will be required to
provide sufficient documentation to verify your identity and legal authorization to work in the United States. Please bring with you on your Start Date, the original of one of the documents noted in List A or one document from List B and one
document from List C as itemized in the enclosed “Lists of Acceptable Documents”. If you do not have the originals of any of these documents, please contact me immediately. 

In the event of any dispute or claim relating to or arising out of your employment relationship with the Company, this agreement, or the
termination of your employment with the Company for any reason (including, but not limited to, any claims of breach of contract, defamation, wrongful termination or age, sex, sexual orientation, race, color, national origin, ancestry, marital
status, religious creed, physical or mental disability or medical condition or other discrimination, retaliation or harassment), you and the Company agree that all such disputes shall be fully resolved by confidential, binding arbitration conducted
by a single arbitrator through the American Arbitration Association (“AAA”) under the AAA’s National Rules for the Resolution of Employment Disputes then in effect, which are available online at the AAA’s website at www.adr.org.
The arbitrator shall permit adequate discovery and is empowered to award all remedies otherwise available in a court of competent jurisdiction and any judgment rendered by the arbitrator may be entered by any court of competent jurisdiction. By
executing this letter, you and the Company are both waiving the right to a jury trial with respect to any such disputes. Company shall bear the costs of the arbitrator, forum and filing fees. Each party shall bear its own respective attorney fees
and all other costs, unless otherwise provided by law and awarded by the arbitrator. 

  
 



 









 



 
 Mr. Frederic Chereau 

December 20, 2013 
 Page four 

 

 It is aTyr’s policy to respect fully the rights of your previous employers in their
proprietary or confidential information. No employee is expected to disclose, or is allowed to use for aTyr’s purposes, any confidential or proprietary information he or she may have acquired as a result of previous employment. 

I am pleased to extend this offer to you and look forward to your acceptance. Please sign and return the enclosed copy of this offer letter as
soon as possible to indicate your agreement with the terms of this offer. This offer will lapse if not signed and returned by December 24, 2013. 

Once signed by you, this letter will constitute the complete agreement between you and aTyr Pharma, Inc. regarding employment matters and will
supersede all prior written or oral agreements or understandings on these matters. 
 Our mission is to discover life-changing therapies
with relentless determination for people with grave maladies where others fall short. I believe you will be able to make an immediate contribution to this mission and I think you will enjoy the rewards of working for an innovative, fast-paced
company. One of the keys to our success is top people. We hope you accept our offer to be one of those people. 
 Yours sincerely, 

/s/ John Mendlein, Ph.D. 
 John Mendlein, Ph.D. 

Executive Chairman and Chief Executive Officer 
 Enclosures 

I accept the terms of employment as described in this offer letter dated
December 20th, 2013 and will start my employment on January 9th, 2014. I confirm that by my start date at aTyr Pharma,
Inc. I will be under no contract or agreement with any other entity which would in any way restrict my ability to work at aTyr Pharma, Inc. or perform the functions of my job for aTyr, including, but, not limited to, any employment agreement and/or
non-compete agreement. 
  

					
	 /s/ Frederic Chereau
	  	
Date 1/09/14                         
               
	  	
	 Frederic Chereau