Document:

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:EX-10.26

 EXHIBIT 10.26 
 THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AND PURSUANT TO
THE PROVISIONS OF ARTICLE 5 BELOW, MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND APPLICABLE STATE SECURITIES LAW OR, IN THE OPINION OF LEGAL COUNSEL IN FORM AND SUBSTANCE
SATISFACTORY TO THE ISSUER OF THESE SECURITIES, SUCH OFFER, SALE OR TRANSFER, PLEDGE OR HYPOTHECATION IS EXEMPT FROM REGISTRATION. 
 WARRANT TO PURCHASE STOCK 
 Company: Tetraphase Pharmaceuticals, Inc., a Delaware
corporation 
 Number of Shares: 233,372, subject to adjustment 
 Class of Stock: Series C Convertible Participating Preferred Stock, $0.001 par value per share 

			
	Warrant Price:	 	$0.2571, subject to adjustment
	Issue Date:	 	February 28, 2013
	Expiration Date:	 	February 27, 2023
	Credit Facility:	 	This Warrant is issued in connection with that certain First Amendment to Loan and Security Agreement dated December 20, 2012 among Silicon Valley Bank, Oxford Finance LLC,
Tetraphase Securities Corporation, and the Company which amended that certain Loan and Security Agreement, dated May 16, 2011 among said parties (as amended, the “Loan Agreement”).

 THIS WARRANT CERTIFIES THAT, for good and valuable consideration, OXFORD FINANCE LLC (“Oxford”
and, together with any successor or permitted assignee or transferee of this Warrant or of any shares issued upon exercise hereof, “Holder”) is entitled to purchase the number of fully paid and non-assessable shares (the
“Shares”) of the above-stated Type/Series of Stock (the “Class”) of the above-named company (the “Company”) at the above-stated Warrant Price, all as set forth above and as
adjusted pursuant to Section 2 of this Warrant, subject to the provisions and upon the terms and conditions set forth in this Warrant. 

ARTICLE 1. EXERCISE. 

1.1 Method of Exercise. Holder may exercise this Warrant by delivering the original of this Warrant together with a duly executed
Notice of Exercise in substantially the form attached as Appendix 1 to the principal office of the Company. Unless Holder is exercising the conversion right set forth in Article 1.2, Holder shall also deliver to the Company a certified or bank
check, wire transfer of immediately available funds (to an account designated by the Company), or other form of payment acceptable to the Company for the aggregate Warrant Price for the Shares being purchased. 

1.2 Conversion Right. In lieu of exercising this Warrant as specified in Article 1.1, Holder may from time to time elect to
convert this Warrant, in whole or in 

 
part, on a cashless basis by delivering the original of this Warrant together with a duly executed Notice of Exercise and by canceling a portion of this Warrant in payment of the Warrant Price
payable in respect of the number of Shares purchased upon such exercise. In the event of an exercise pursuant to this Article 1.2, the number of Shares issued to the holder shall be determined by dividing (a) the aggregate fair market value of
the Shares for which this Warrant is being exercised (which shall include both the number of Shares issued to the Holder and the number of Shares subject to the portion of the Warrant being cancelled) minus the aggregate Warrant Price of such Shares
by (b) the fair market value of one Share. The fair market value of the Shares shall be determined pursuant to Article 1.3. 
 1.3 Fair Market Value. If the Company’s common stock is then traded or quoted on a nationally recognized securities exchange, inter-dealer quotation system or over-the-counter market (a
“Trading Market”) and the Class is common stock, the fair market value of a Share shall be the closing price or last sale price of a share of common stock reported for the Business Day immediately before the date on which Holder delivers
this Warrant together with its Notice of Exercise to the Company. If the Company’s common stock is then traded in a Trading Market and the Class is a series of the Company’s convertible preferred stock, the fair market value of a Share
shall be the closing price or last sale price of a share of the Company’s common stock reported for the Business Day immediately before the date on which Holder delivers this Warrant together with its Notice of Exercise to the Company
multiplied by the number of shares of the Company’s common stock into which a Share is then convertible. If the Company’s common stock is not traded in a Trading Market, the Board of Directors of the Company shall determine the fair market
value of a Share in its reasonable good faith judgment. 
 1.4 Delivery of Certificate and New Warrant. Promptly after
Holder exercises or converts this Warrant and, if applicable, the Company receives payment of the aggregate Warrant Price, the Company shall deliver to Holder certificates for the Shares acquired and, if this Warrant has not been fully exercised or
converted and has not expired, a new Warrant representing the Shares not so acquired. 
 1.5 Replacement of Warrants. On
receipt of evidence reasonably satisfactory to the Company of the loss, theft, destruction or mutilation of this Warrant and, in the case of loss, theft or destruction, on delivery of an indemnity agreement reasonably satisfactory in form and amount
to the Company or, in the case of mutilation, on surrender and cancellation of this Warrant, the Company shall execute and deliver, in lieu of this Warrant, a new warrant of like tenor. 

1.6 Treatment of Warrant Upon Acquisition of Company. 
 1.6.1 “Acquisition”. For the purpose of this Warrant, “Acquisition” means any sale, license, or other disposition of all or substantially all of the assets of the Company, or
any reorganization, consolidation, merger or sale of outstanding capital stock of the Company where the holders of the Company’s securities before the transaction beneficially own less than a majority of the outstanding voting securities of the
surviving entity after the transaction. 

  
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 1.6.2 Treatment of Warrant at Acquisition. 

A) Holder agrees that, in the event of an Acquisition in which the consideration is solely cash, solely Marketable Securities, or a combination of cash
and Marketable Securities, Holder shall either (a) exercise its conversion or purchase right under this Warrant and such exercise will be deemed effective immediately prior to the closing of such Acquisition and any part of this Warrant not
exercised by the closing of such Acquisition will expire or (b) elect not to exercise its conversion or purchase right under this Warrant, in which case this Warrant will expire upon the closing of such Acquisition. The Company shall provide
the Holder with written notice of any Acquisition (together with such reasonable information as the Holder may request in connection with such Acquisition) not less than ten (10) days prior to the closing of the proposed Acquisition.

 B) Holder agrees that, in the event of an Acquisition that is an “arms length” sale of all or substantially all of the
Company’s assets to a third party that is not an Affiliate (as defined below) of the Company (a “True Asset Sale”), Holder shall exercise its conversion or purchase right under this Warrant and such exercise will be deemed effective
immediately prior to the closing of such Acquisition and any part of this Warrant not exercised by the closing of such Acquisition will expire; provided, however, that if the Company continues as a going concern following the closing of any such
True Asset Sale and Holder elects not to exercise the Warrant, this Warrant will continue to be exercisable until the Expiration Date. The Company shall provide the Holder with such reasonable information as the Holder may request in connection with
such contemplated Acquisition, which is to be delivered to Holder not less than ten (10) days prior to the closing of the proposed Acquisition. 
 C) Upon the closing of any Acquisition other than those particularly described in subsections (A) and (B) above, the successor entity shall assume the obligations of this Warrant, and this
Warrant shall be exercisable for the same securities, cash, and property as would be payable for the Shares issuable upon exercise of the unexercised portion of this Warrant as if such Shares were outstanding on the record date for the Acquisition
and subsequent closing. The Warrant Price and/or number of Shares shall be adjusted accordingly. 
 As used herein “Affiliate” shall
mean any person or entity that owns or controls directly or indirectly ten percent (10%) or more of the stock of Company, any person or entity that controls or is controlled by or is under common control with such persons or entities, and each
of such person’s or entity’s officers, directors, joint venturers or partners, as applicable. 
 As used herein, “Marketable
Securities” means securities meeting all of the following requirements: (i) the issuer thereof is then subject to the reporting requirements of Section 13 or Section 15(d) of the Securities Exchange Act of 1934, as amended (the
“Exchange Act”), and is then current in its filing of all required reports and other information under the Act and the Exchange Act; (ii) the class and series of shares or other security of the issuer that would be received by Holder
in connection with the Acquisition were Holder to exercise this Warrant on or prior to the closing thereof is then traded in Trading Market, and (iii) following the closing of such Acquisition, Holder would not be restricted from publicly
re-selling all of the issuer’s shares and/or other securities that would be received by Holder in such Acquisition were Holder to exercise or convert this Warrant in full on or prior to the closing of such Acquisition, except to the extent that

  
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any such restriction (x) arises solely under federal or state securities laws, rules or regulations, and (y) does not extend beyond six (6) months from the closing of such
Acquisition. 
 ARTICLE 2. ADJUSTMENTS TO THE SHARES. 
 2.1 Stock Dividends, Splits, Etc. If the Company declares or pays a dividend on the outstanding shares of the Class payable in Common Stock or other securities, then upon exercise of this Warrant,
for each Share acquired, Holder shall receive, without cost to Holder, the total number and kind of securities to which Holder would have been entitled had Holder owned the Shares as of the record date for the dividend. If the Company subdivides the
outstanding shares of the Class by reclassification or otherwise into a greater number of shares or takes any other action which increase the amount of Common Stock into which the one share of the Class is convertible, the number of Shares
purchasable hereunder shall be proportionately increased and the Warrant Price shall be proportionately decreased. If the outstanding shares of the Class are combined or consolidated, by reclassification or otherwise, into a lesser number of shares
of the Class, the Warrant Price shall be proportionately increased and the number of Shares shall be proportionately decreased. 

2.2 Reclassification, Exchange, Combinations or Substitution. Upon any reclassification, exchange, substitution, or other event
that results in a change of the number and/or class of the securities issuable upon exercise or conversion of this Warrant (other than those transactions contemplated by Article 1.6 or Article 2.1), Holder shall be entitled to receive, upon exercise
or conversion of this Warrant, the number and kind of securities and property that Holder would have received for the Shares if this Warrant had been exercised immediately before such reclassification, exchange, substitution, or other event. Such an
event shall include, without limitation, any automatic conversion of the outstanding or issuable securities of the Company of the same class or series as the Shares to Common Stock pursuant to the terms of the Company’s Amended and Restated
Certificate of Incorporation, as amended from time to time (the “Certificate of Incorporation”). The Company or its successor shall promptly issue to Holder an amendment to this Warrant setting forth the number and kind of such new
securities or other property issuable upon exercise or conversion of this Warrant as a result of such reclassification, exchange, substitution or other event that results in a change of the number and/or class of securities issuable upon exercise or
conversion of this Warrant. The amendment to this Warrant shall provide for adjustments which shall be as nearly equivalent as may be practicable to the adjustments provided for in this Article 2 including, without limitation, adjustments to the
Warrant Price and to the number of securities or property issuable upon exercise of the new Warrant. The provisions of this Article 2.2 shall similarly apply to successive reclassifications, exchanges, substitutions, or other events. 

2.3 Adjustments for Diluting Issuances. The number of shares of Common Stock issuable upon conversion of the Shares shall be
subject to adjustment, from time to time in the manner set forth in the Certificate of Incorporation as if the Shares were issued and outstanding on and as of the date of any such required adjustment. The provisions set forth for the Class in the
Certificate of Incorporation relating to the above in effect as of the Issue Date may not be amended, modified or waived, without the prior written consent of Holder unless such amendment, modification or waiver affects the rights associated with
the Shares in the same manner as such amendment, modification or waiver affects the rights associated with all other shares of Class. 

  
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 2.4 No Impairment. The Company shall not, by amendment of its Certificate of
Incorporation or through a reorganization, transfer of assets, consolidation, merger, dissolution, issue, or sale of securities or any other voluntary action, avoid or seek to avoid the observance or performance of any of the terms to be observed or
performed under this Warrant by the Company, but shall at all times in good faith assist in carrying out of all the provisions of this Article 2 and in taking all such action as may be necessary or appropriate to protect Holder’s rights under
this Article against impairment. 
 2.5 Fractional Shares. No fractional Shares shall be issuable upon exercise or
conversion of the Warrant and the number of Shares to be issued shall be rounded down to the nearest whole Share. If a fractional share interest arises upon any exercise or conversion of the Warrant, the Company shall eliminate such fractional share
interest by paying Holder the amount computed by multiplying the fractional interest by the fair market value of a full Share. 

2.6 Certificate as to Adjustments. Upon each adjustment of the Warrant Price, Class and/or number of Shares, the Company shall
promptly notify Holder in writing, and, at the Company’s expense, promptly compute such adjustment, and furnish Holder with a certificate of its Chief Financial Officer setting forth such adjustment and the facts upon which such adjustment is
based. The Company shall, upon written request, furnish Holder a certificate setting forth the Warrant Price, Class and number of Shares in effect upon the date thereof and the series of adjustments leading to such Warrant Price, Class and number of
Shares. 
 ARTICLE 3. REPRESENTATIONS AND COVENANTS OF THE COMPANY. 

3.1 Representations and Warranties. The Company represents and warrants to, and agrees with, the Holder as follows, as of the
Issue Date: 
 (a) The initial Warrant Price referenced on the first page of this Warrant is not greater than the price per
share at which shares of the same class and series as the Shares were last issued in an arms-length transaction in which at least $500,000 of such shares were sold. 
 (b) All Shares which may be issued upon the exercise of the purchase right represented by this Warrant, and all securities, if any, issuable upon conversion of the Shares, shall, upon issuance, be duly
authorized, validly issued, fully paid and nonassessable, and free of any liens and encumbrances except for restrictions on transfer provided for herein or under applicable federal and state securities laws. 

(c) The Company’s capitalization table attached hereto as Schedule 1 is true and complete as of the Issue Date. 

3.2 Notice of Certain Events. If the Company proposes at any time (a) to declare any dividend or distribution upon the
outstanding shares of the same class and series as the Shares, whether in cash, property, stock, or other securities and whether or not a regular cash dividend; (b) to offer for subscription or sale pro rata to the

  
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holders of the outstanding shares of the same class and series as the Shares any additional shares of any class or series of the Company’s stock (other than pursuant to contractual
pre-emptive rights); (c) to effect any reclassification, reorganization or recapitalization of any of its stock; (d) to effect an Acquisition or to liquidate, dissolve or wind up; or (e) offer holders of registration rights the
opportunity to participate in an underwritten public offering of the company’s securities for cash, then, in connection with each such event, the Company shall give Holder: (1) at least 10 days prior written notice of the date on which a
record will be taken for such dividend, distribution, or subscription rights (and specifying the date on which the holders of shares of the same class and series as the Shares will be entitled thereto) or for determining rights to vote, if any, in
respect of the matters referred to in (c) and (d) above; (2) in the case of the matters referred to in (c) and (d) above at least 10 days prior written notice of the date when the same will take place (and specifying the
date on which the holders of shares of the same class and series as the Shares will be entitled to exchange their shares for the securities or other property deliverable upon the occurrence of such event); and (3) in the case of the matter
referred to in (e) above, the same notice as is given to the holders of such registration rights. 
 3.3 Intentionally
Omitted. 
 3.4 No Shareholder Rights. Except as provided in this Warrant, Holder will not have any rights as a
shareholder of the Company until the exercise of this Warrant. 
 3.5 Certain Information. At all times prior to the
earlier to occur of (i) the IPO, or (ii) the Acquisition of the Company by an entity subject to the reporting requirements of Section 13 or Section 15(d) of the Securities Exchange Act of 1934, as amended, the Company agrees to
provide Holder at any time and from time to time with such information as Holder may reasonably request for purposes of Holder’s compliance with regulatory, accounting and reporting requirements applicable to Holder. Holder agrees to treat and
hold all such information provided by the Company in confidence in accordance with the provisions of Section 12.9 of the Loan Agreement (regardless of whether the Loan Agreement is still then in force and effect). 

ARTICLE 4. REPRESENTATIONS, WARRANTIES OF THE HOLDER. The Holder represents and warrants to the Company as follows: 

4.1 Purchase for Own Account. This Warrant and the securities to be acquired upon exercise of this Warrant by Holder will be
acquired for investment for Holder’s account, not as a nominee or agent, and not with a view to the public resale or distribution within the meaning of the Act. Holder also represents that it has not been formed for the specific purpose of
acquiring this Warrant or the Shares. 
 4.2 Disclosure of Information. Holder has received or has had full access to all
the information it considers necessary or appropriate to make an informed investment decision with respect to the acquisition of this Warrant and its underlying securities. Holder further has had an opportunity to ask questions and receive answers
from the Company regarding the terms and conditions of the offering of this Warrant and its underlying securities and to obtain additional information (to the extent the Company possessed such information or could acquire it without unreasonable
effort or expense) necessary to verify any information furnished to Holder or to which Holder has access. 

  
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 4.3 Investment Experience. Holder understands that the purchase of this Warrant and
its underlying securities involves substantial risk. Holder has experience as an investor in securities of companies in the development stage and acknowledges that Holder can bear the economic risk of such Holder’s investment in this Warrant
and its underlying securities and has such knowledge and experience in financial or business matters that Holder is capable of evaluating the merits and risks of its investment in this Warrant and its underlying securities and/or has a preexisting
personal or business relationship with the Company and certain of its officers, directors or controlling persons of a nature and duration that enables Holder to be aware of the character, business acumen and financial circumstances of such persons.

 4.4 Accredited Investor Status. Holder is an “accredited investor” within the meaning of Regulation D
promulgated under the Act. 
 4.5 The Act. Holder understands that this Warrant and the Shares issuable upon exercise or
conversion hereof have not been registered under the Act in reliance upon a specific exemption therefrom, which exemption depends upon, among other things, the bona fide nature of the Holder’s investment intent as expressed herein. Holder
understands that this Warrant and the Shares issued upon any exercise or conversion hereof must be held indefinitely unless subsequently registered under the Act and qualified under applicable state securities laws, or unless exemption from such
registration and qualification are otherwise available. 
 4.6 Lockup Agreements. The Holder, if the Company or the
managing underwriter(s) so request in connection with the Company’s initial underwritten public offering, will not, transfer or dispose of any equity securities of the Company, without the prior written consent of the Company or such
underwriter(s) and provided that the officers and directors of the Company and all holders (other than, for purposes of this determination, such Holder) of at least two percent (2%) of all of the issued and outstanding shares of capital
stock of the Company (determined on an as-converted basis) also agree not to, transfer or dispose any equity securities of the Company, including any sale pursuant to Rule 144 of the Commission under the Securities Act, during the seven
(7) days prior to, and during the one hundred eighty (180) day period commencing on the effective date of such initial underwritten public offering, subject to extension in order to ensure FINRA compliance, except in connection with such
initial underwritten public offering. The Company may impose stop-transfer instructions with respect to the Shares or other securities subject to the foregoing restriction until the end of such 180-day period. Any discretionary waiver or termination
of the foregoing restriction by the Company or the underwriters shall apply pro rata to all Holders, based on the number of Shares held by such Holders, and prompt written notice of such discretionary waiver or termination shall be given to all
Holders of the Shares. 
 ARTICLE 5. MISCELLANEOUS. 
 5.1 Term: This Warrant is exercisable in whole or in part at any time and from time to time on or before the Expiration Date. 

  
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 5.2 Legends. This Warrant and the Shares (and the securities issuable, directly or
indirectly, upon conversion of the Shares, if any) shall be imprinted with a legend in substantially the following form: 
 THIS
WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE ACT, OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AND PURSUANT TO THE PROVISIONS OF ARTICLE 5 OF THAT CERTAIN WARRANT TO PURCHASE STOCK ISSUED BY THE COMPANY TO OXFORD
FINANCE LLC DATED AS OF FEBRUARY 28, 2013, MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND APPLICABLE STATE SECURITIES LAW OR, IN THE OPINION OF LEGAL COUNSEL IN FORM AND
SUBSTANCE SATISFACTORY TO THE ISSUER OF THESE SECURITIES, SUCH OFFER, SALE OR TRANSFER, PLEDGE OR HYPOTHECATION IS EXEMPT FROM REGISTRATION. 
 5.3 Compliance with Securities Laws on Transfer. This Warrant and the Shares issuable upon exercise of this Warrant (and the securities issuable, directly or indirectly, upon conversion of the
Shares, if any) may not be transferred or assigned in whole or in part without compliance with applicable federal and state securities laws by the transferor and the transferee (including, without limitation, the delivery of investment
representation letters and legal opinions reasonably satisfactory to the Company, as reasonably requested by the Company). The Company shall not require Holder to provide an opinion of counsel if the transfer is to any affiliate of Holder, provided
that any such transferee is an “accredited investor” as defined in Regulation D promulgated under the Act. 
 5.4
Transfer Procedure. Following the issuance of this Warrant to Oxford, Oxford may transfer same in whole or in part to one or more affiliates of Oxford, and in connection with any such transfer Oxford and the affiliate transferee shall execute
and deliver to the Company an Assignment substantially in the form of Appendix 2 hereto. Subject to the provisions of Section 5.3 and upon providing the Company with written notice, such Oxford affiliate and any subsequent Holder may transfer
all or part of this Warrant or the Shares issued upon exercise of this Warrant (or the securities issued upon conversion of the Shares, if any) to any transferee, provided, however, in connection with any such transfer, such Oxford affiliate or any
subsequent Holder will give the Company notice of the portion of the Warrant and/or Shares (and/or securities issued upon conversion of the Shares, if any) being transferred with the name, address and taxpayer identification number of the transferee
and Holder will surrender this Warrant to the Company for reissuance to the transferee(s) (and Holder if applicable). Notwithstanding any contrary provision herein, at all times prior to the IPO, Holder may not, without the Company’s prior
written consent, transfer this Warrant or any portion hereof, or any Shares issued upon any exercise hereof, or any shares or other securities issued upon any conversion of any Shares issued upon any exercise hereof, to any person or entity who
directly competes with the Company, except in connection with an Acquisition of the Company by such a direct competitor. 

  
 8 

 5.5 Notices. All notices and other communications from the Company to the Holder, or
vice versa, shall be deemed delivered and effective when given personally or mailed by first-class registered or certified mail, postage prepaid, at such address as may have been furnished to the Company or Holder, as the case may (or on the first
Business Day after transmission by facsimile) be, in writing by the Company or such holder from time to time. All notices to Holder shall be addressed as follows until the Company receives notice of a change of address in connection with a transfer
or otherwise: 
 Oxford Finance LLC 
 Attn: Ms. Maryam Zafar, Senior Counsel 
 133 North Fairfax Street 

Alexandria, VA 22314 
 Facsimile: 703-519-6015 
 Email address: mzafar@oxfordfinance.com 

Notice to the Company shall be addressed as follows until Holder receives notice of a change in address: 

Tetraphase Pharmaceuticals, Inc. 
 Attn: Chief Operating Officer 
 480 Arsenal Street, Suite 110 

Watertown, MA 02462 
 Telephone: 617-715-3551 
 Facsimile: 617-715-3557 

5.6 Amendment and Waiver. This Warrant and any term hereof may be amended, waived, discharged or terminated only by an instrument
in writing signed by the Company and the Holder. 
 5.7 Attorney’s Fees. In the event of any dispute between the
parties concerning the terms and provisions of this Warrant, the party prevailing in such dispute shall be entitled to collect from the other party all costs incurred in such dispute, including reasonable attorneys’ fees. 

5.8 Automatic Conversion upon Expiration. In the event that, upon the Expiration Date, the fair market value of one Share (or
other security issuable upon the exercise hereof) as determined in accordance with Article 1.3 above is greater than the Warrant Price in effect on such date, then this Warrant shall automatically be deemed on and as of such date to be converted
pursuant to Article 1.2 above as to all Shares (or such other securities) for which it shall not previously have been exercised or converted, and the Company shall promptly deliver a certificate representing the Shares (or such other securities)
issued upon such conversion to Holder. 
 5.9 Counterparts. This Warrant may be executed in counterparts, all of which
together shall constitute one and the same agreement. 

  
 9 

 5.10 Governing Law. This Warrant shall be governed by and construed in accordance
with the laws of the State of Delaware, without giving effect to its principles regarding conflicts of law. 
 5.11 Business
Days. “Business Day” is any day that is not a Saturday, Sunday or a day on which Oxford is closed. 
  

			
	“COMPANY”
	
	TETRAPHASE PHARMACEUTICALS, INC.
		
	By:	 	 /s/ David Lubner

		
	Name:	 	 David Lubner

		 	(Print)
	Title:	 	Senior Vice President and Chief Financial Officer

  

			
	“HOLDER”
	
	OXFORD FINANCE LLC
		
	By:	 	 /s/ Mark Davis

		
	Name:	 	 Mark Davis

		 	(Print)
	Title:	 	Vice President – Finance, Secretary & Treasurer

  
 10 

 APPENDIX 1 
 NOTICE OF EXERCISE 
 1. Holder elects to purchase
                 shares of the Common/Series                     
Preferred [strike one] Stock of                      pursuant to the terms of the attached Warrant, and tenders payment of the purchase price of the
shares in full. 
 [or] 
 1. Holder elects to convert the attached Warrant into Shares/cash [strike one] in the manner specified in the Warrant. This conversion is exercised for
                                         of the
Shares covered by the Warrant. 
 [Strike paragraph that does not apply.] 

2. Please issue a certificate or certificates representing the shares in the name specified below: 

 

	
	  

	 Holders Name

	
	  

	
	  

	 (Address)

 3. By its execution below and for the benefit of the Company, Holder hereby restates each of the
representations and warranties in Article 4 of the Warrant as the date hereof. 
  

			
	HOLDER:
	
	  

		
	By:	 	  

		
	Name:	 	  

		
	Title:	 	  

		
	(Date):	 	  

  
 Appendix 1 - 1

 APPENDIX 2 
 FORM OF ASSIGNMENT 
 For value received, Oxford Finance LLC hereby sells, assigns
and transfers unto 
  

							
		  	Name: [OXFORD TRANSFEREE]	  	
		  	Address:	  	  
	  	
		  		  	  
	  	
		  	Tax ID:	  	  
	  	

 that certain Warrant to Purchase Stock issued by [BORROWER] (the “Company”), on [ISSUE DATE] (the
“Warrant”) together with all rights, title and interest therein. 
  

			
	OXFORD FINANCE LLC
		
	By:	 	  

	Name:	 	  

	Title:	 	  

  

			
	Date:	 	  

 By its execution below, and for the benefit of the Company, [OXFORD TRANSFEREE] hereby makes each of the representations
and warranties set forth in Article 4 of the Warrant as of the date hereof and agrees to be bound by all provisions of the Warrant as the Holder thereof. 

 

			
	[OXFORD TRANSFEREE]
		
	By:	 	  

	Name:	 	  

	Title:	 	  

  
 Appendix 2 - 1

 SCHEDULE 1 
 Company Capitalization Table 
 Tetraphase Pharmaceuticals, Inc. 

 

									
	 Type of Security
	  	Number of Authorized
Shares	 	  	Number of Outstanding
Shares	 
	 Common Stock
	  	 	317,789,510	  	  	 	9,432,466	  
	 Series A-1 Convertible Participating Preferred Stock
	  	 	10,072,000	  	  	 	10,040,000	  
	 Series A-2 Convertible Participating Preferred Stock
	  	 	13,095,646	  	  	 	13,095,646	  
	 Series B Convertible Participating Preferred Stock
	  	 	57,471,225	  	  	 	57,471,225	  
	 Series C Convertible Participating Preferred Stock
	  	 	178,405,286	  	  	 	175,418,122	  

  
 Schedule 1 - 1

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