EX-10.10



 EXHIBIT 10.10 
 TETRAPHASE PHARMACEUTICALS, INC. 
 NONSTATUTORY STOCK OPTION AGREEMENT 
 GRANTED UNDER 2013 STOCK INCENTIVE PLAN 
  

	1.	Grant of Option. 

 This
agreement evidences the grant by Tetraphase Pharmaceuticals, Inc., a Delaware corporation (the “Company”), on                     ,
201     (the “Grant Date”) to                     , [an employee of / a director of / a consultant to / an advisor to]
the Company (the “Participant”), of an option to purchase, in whole or in part, on the terms provided herein and in the Company’s 2013 Stock Incentive Plan (the “Plan”), a total of
                 shares (the “Shares”) of common stock, par value $0.001 per share, of the Company (“Common Stock”) at a price of
$             per Share. Unless earlier terminated, this option shall expire at 5:00 p.m., Eastern time, on
                     (the “Final Exercise Date”). 
 It is intended that the option evidenced by this agreement shall not be an incentive stock option as defined in Section 422 of the Internal Revenue Code of 1986, as amended, and any regulations
promulgated thereunder (the “Code”). Except as otherwise indicated by the context, the term “Participant”, as used in this option, shall be deemed to include any person who acquires the right to exercise this option validly under
its terms. 
  

	2.	Vesting Schedule. 

 This
option will become exercisable (“vest”) as follows:
                                        

 The right of exercise shall be cumulative so that to the extent the option is not exercised in any period to the maximum
extent permissible it shall continue to be exercisable, in whole or in part, with respect to all Shares for which it is vested until the earlier of the Final Exercise Date or the termination of this option under Section 3 hereof or the Plan.

  

	3.	Exercise of Option. 

 (a)
Form of Exercise. Each election to exercise this option shall be in writing, signed by the Participant, and received by the Company at its principal office, accompanied by this agreement, and payment in full in the manner provided in the Plan
or indication on such notice of exercise that the Participant wishes to effect a net exercise of this option in accordance with Section 5(f)(4) of the Plan. The Participant may purchase less than the number of shares covered hereby, provided
that no partial exercise of this option may be for any fractional share. 
 (b) Continuous Relationship with the Company
Required. Except as otherwise provided in this Section 3, this option may not be exercised unless the Participant, at the time he or she exercises this option, is, and has been at all times since the Grant Date, an employee or director of,
or consultant or advisor to, the Company or any other entity the employees, officers, directors, consultants or advisors of which are eligible to receive option grants under the Plan (an “Eligible Participant”). 







 (c) Termination of Relationship with the Company. If the Participant ceases to be an
Eligible Participant for any reason, then, except as provided in paragraphs (d) and (e) below, the right to exercise this option shall terminate three months after such cessation (but in no event after the Final Exercise Date),
provided that this option shall be exercisable only to the extent that the Participant was entitled to exercise this option on the date of such cessation. Notwithstanding the foregoing, if the Participant, prior to the Final Exercise
Date, violates the non-competition or confidentiality provisions of any employment contract, confidentiality and nondisclosure agreement or other agreement between the Participant and the Company, the right to exercise this option shall terminate
immediately upon written notice to the Participant from the Company describing such violation. 
 (d) Exercise Period Upon
Death or Disability. If the Participant dies or becomes disabled (within the meaning of Section 22(e)(3) of the Code) prior to the Final Exercise Date while he or she is an Eligible Participant and the Company has not terminated such
relationship for “cause” as specified in paragraph (e) below, this option shall be exercisable, within the period of one year following the date of death or disability of the Participant, by the Participant (or in the case of death by
an authorized transferee), provided that this option shall be exercisable only to the extent that this option was exercisable by the Participant on the date of his or her death or disability, and further provided that this option shall
not be exercisable after the Final Exercise Date. 
 (e) Termination for Cause. If, prior to the Final Exercise Date, the
Participant’s employment or other relationship with the Company is terminated by the Company for Cause (as defined below), the right to exercise this option shall terminate immediately upon the effective date of such termination of employment
or other relationship. If, prior to the Final Exercise Date, the Participant is given notice by the Company of the termination of his or her employment or other relationship by the Company for Cause, and the effective date of such employment or
other termination is subsequent to the date of the delivery of such notice, the right to exercise this option shall be suspended from the time of the delivery of such notice until the earlier of (i) such time as it is determined or otherwise
agreed that the Participant’s employment or other relationship shall not be terminated for Cause as provided in such notice or (ii) the effective date of such termination of employment or other relationship (in which case the right to
exercise this option shall, pursuant to the preceding sentence, terminate immediately upon the effective date of such termination of employment or other relationship). If the Participant is party to an employment, consulting or severance agreement
with the Company that contains a definition of “cause” for termination of employment or other relationship, “Cause” shall have the meaning ascribed to such term in such agreement. Otherwise, “Cause” shall mean willful
misconduct by the Participant or willful failure by the Participant to perform his or her responsibilities to the Company (including, without limitation, breach by the Participant of any provision of any employment, consulting, advisory,
nondisclosure, non-competition or other similar agreement between the Participant and the Company), as determined by the Company, which determination shall be conclusive. The Participant’s employment or other relationship shall be considered to
have been terminated for “Cause” if the Company determines, within 30 days after the Participant’s resignation, that termination for Cause was warranted. 

  
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	4.	Withholding. 

 No Shares
will be issued pursuant to the exercise of this option unless and until the Participant pays to the Company, or makes provision satisfactory to the Company for payment of, any federal, state or local withholding taxes required by law to be withheld
in respect of this option. 
  

	5.	Transfer Restrictions. 


This option may not be sold, assigned, transferred, pledged or otherwise encumbered by the Participant, either voluntarily or by operation
of law, except by will or the laws of descent and distribution, and, during the lifetime of the Participant, this option shall be exercisable only by the Participant. 
  

	6.	Provisions of the Plan. 


This option is subject to the provisions of the Plan (including the provisions relating to amendments to the Plan), a copy of which is
furnished to the Participant with this option. 
 IN WITNESS WHEREOF, the Company has caused this option to be executed under
its corporate seal by its duly authorized officer. This option shall take effect as a sealed instrument. 
  

					
	TETRAPHASE PHARMACEUTICALS, INC. 
		
	By:	 	  

			
		 	Name:	 	  

		 	Title:	 	  




  
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 PARTICIPANT’S ACCEPTANCE 

The undersigned hereby accepts the foregoing option and agrees to the terms and conditions thereof. The undersigned hereby acknowledges
receipt of a copy of the Company’s 2013 Stock Incentive Plan. 
  

			
	PARTICIPANT:
	
	  

		
	Address:	 	  

		
		 	  




  
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 FORM OF NOTICE OF STOCK OPTION EXERCISE 

Date:
                     
 Tetraphase
Pharmaceuticals, Inc. 
 480 Arsenal Street, Suite 110 
 Watertown, MA 02472 
 Attention: Treasurer 

Dear Sir or Madam: 
 I am the
holder of a Nonstatutory Stock Option granted to me under the Tetraphase Pharmaceuticals, Inc. (the “Company”) 2013 Stock Incentive Plan (the “Plan”) on
                     for the purchase of                  shares of
common stock, par value $0.001 per share, of the Company (“Common Stock”) at a purchase price of $             per share. 

I hereby exercise my option with respect to
                 shares of Common Stock for which: 
 (Select as
appropriate) 
  ̈  I have enclosed
                     in the amount of
                                        .

  ̈  I wish to effect a net exercise in accordance with Section 5(f)(4) of the
Plan, and in connection therewith I understand that I will receive fewer than the number of shares set forth above with respect to which I am exercising my option. 
 Please register my stock certificate as follows: 
  

							
	Name(s):	 	  
	 		 	
				
		 	  
	 		 	
				
	Address:	 	  
	 		 	
				
	Tax I.D. #:	 	  
	 		 	

  

			
	Very truly yours,
	
	  

	Name: