EX-10.9



 EXHIBIT 10.9 
 TETRAPHASE PHARMACEUTICALS, INC. 
 INCENTIVE 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 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 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. The Participant may exercise this option for 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 officer of, or consultant or advisor to, the Company or any parent or subsidiary of the Company as
defined in Section 424(e) or (f) of the Code (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 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. If, prior to the Final Exercise Date, the Participant is given notice by the Company
of the termination of his or her employment by the Company for Cause, and the effective date of such employment termination is subsequent to the date of 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 shall not be terminated for Cause as provided in such notice or (ii) the effective date of such
termination of employment (in which case the right to exercise this option shall, pursuant to the preceding sentence, terminate upon the effective date of such termination of employment). If the Participant is party to an employment or severance
agreement with the Company that contains a definition of “cause” for termination of employment, “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 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. 
  

	4.	Tax Matters. 

 (a)
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. 

  
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 (b) Disqualifying Disposition. If the Participant disposes of Shares acquired upon
exercise of this option within two years from the Grant Date or one year after such Shares were acquired pursuant to exercise of this option, the Participant shall notify the Company in writing of such disposition. 

 

	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 an Incentive Stock Option granted to me under the Tetraphase Pharmaceuticals, Inc. (the “Company”) 2013 Stock Incentive 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 I have enclosed
                     in the amount of
                    . Please register my stock certificate as follows: 

 

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

  

			
	Very truly yours,
	
	  

	Name: