Document:

2010 Employee Stock Purchase Plan

 Exhibit 10.5 
 TRIUS THERAPEUTICS, INC. 
 2010 EMPLOYEE STOCK PURCHASE PLAN 
 ADOPTED BY THE BOARD OF DIRECTORS:
[                    ], 2009 
 APPROVED BY THE STOCKHOLDERS:
[                    ], 2009 
  

	1.	 GENERAL. 

 (a) The purpose of the Plan is to provide a means by which Eligible Employees of the Company and certain designated Related Corporations may be given an opportunity to purchase shares of Common
Stock. The Plan is intended to permit the Company to grant a series of Purchase Rights to Eligible Employees under an Employee Stock Purchase Plan. 
 (b) The Company, by means of the Plan, seeks to retain the services of such Employees, to secure and retain the services of new Employees and to provide incentives for such persons to exert maximum
efforts for the success of the Company and its Related Corporations. 
  

	2.	 ADMINISTRATION. 

 (a) The Board shall administer the Plan unless and until the Board delegates administration of the Plan to a Committee or Committees, as provided in Section 2(c).

 (b) The Board shall have the power, subject to, and within the limitations of, the express provisions
of the Plan: 
 (i) To determine how and when Purchase Rights to purchase shares of Common Stock shall be
granted and the provisions of each Offering of such Purchase Rights (which need not be identical). 
 (ii) To designate from time to time which Related Corporations of the Company shall be eligible to participate in the Plan. 
 (iii) To construe and interpret the Plan and Purchase Rights, and to establish, amend and revoke rules and regulations for its administration. The Board, in the exercise of this power, may correct
any defect, omission or inconsistency in the Plan, in a manner and to the extent it shall deem necessary or expedient to make the Plan fully effective. 
 (iv) To settle all controversies regarding the Plan and Purchase Rights granted under it. 
 (v) To suspend or terminate the Plan at any time as provided in Section 12. 
 (vi) To amend the Plan at any time as provided in Section 12. 
 (vii) Generally, to exercise such powers and to perform such acts as it deems necessary or expedient to promote the best interests of the Company and its Related Corporations and to carry out the intent that the Plan be treated as an
Employee Stock Purchase Plan. 
  

 1. 

 (viii) To adopt such procedures and sub-plans as are necessary or
appropriate to permit participation in the Plan by Employees who are foreign nationals or employed outside the United States. 
 (c) The Board may delegate some or all of the administration of the Plan to a Committee or Committees. If administration is delegated to a Committee, the Committee shall have, in connection with
the administration of the Plan, the powers theretofore possessed by the Board that have been delegated to the Committee, including the power to delegate to a subcommittee any of the administrative powers the Committee is authorized to exercise (and
references in this Plan to the Board shall thereafter be to the Committee or subcommittee), subject, however, to such resolutions, not inconsistent with the provisions of the Plan, as may be adopted from time to time by the Board. The Board may
retain the authority to concurrently administer the Plan with the Committee and may, at any time, revest in the Board some or all of the powers previously delegated. Whether or not the Board has delegated administration of the Plan to a Committee,
the Board shall have the final power to determine all questions of policy and expediency that may arise in the administration of the Plan. 
 (d) All determinations, interpretations and constructions made by the Board in good faith shall not be subject to review by any person and shall be final, binding and conclusive on all persons.

  

	3.	 SHARES OF COMMON STOCK SUBJECT TO THE
PLAN. 

 (a) Subject to the provisions of
Section 11(a) relating to Capitalization Adjustments, the shares of Common Stock that may be sold pursuant to Purchase Rights shall not exceed in the aggregate [            ]
shares of Common Stock. In addition, the number of shares of Common Stock available for issuance under the Plan shall automatically increase on January 1st of each year, commencing in 2011 and ending on (and including) January 1, 2020, in an amount equal to the lesser
of (i) [            ]% of the total number of shares of Common Stock outstanding on December 31st of the preceding calendar year, or
(ii) [            ] shares of Common Stock. Notwithstanding the foregoing, the Board may act prior to the first day of any calendar year, to provide that there shall be no
increase in the share reserve for such calendar year or that the increase in the share reserve for such calendar year shall be a lesser number of shares of Common Stock than would otherwise occur pursuant to the preceding sentence. 
 (b) If any Purchase Right granted under the Plan shall for any reason terminate without having been exercised, the
shares of Common Stock not purchased under such Purchase Right shall again become available for issuance under the Plan. 
 (c) The stock purchasable under the Plan shall be shares of authorized but unissued or reacquired Common Stock, including shares repurchased by the Company on the open market. 
  

	4.	 GRANT OF PURCHASE RIGHTS; OFFERING. 

(a) The Board may from time to time grant or provide for the grant of Purchase Rights to purchase shares of Common
Stock under the Plan to Eligible Employees in an Offering (consisting of one or more Purchase Periods) on an Offering Date or Offering Dates selected by the Board. Each Offering shall be in such form and shall contain such terms and conditions as
the Board shall deem

  

 2. 

 
appropriate, which shall comply with the requirement of Section 423(b)(5) of the Code that all Employees granted Purchase Rights shall have the same rights and privileges. The terms and
conditions of an Offering shall be incorporated by reference into the Plan and treated as part of the Plan. The provisions of separate Offerings need not be identical, but each Offering shall include (through incorporation of the provisions of this
Plan by reference in the document comprising the Offering or otherwise) the period during which the Offering shall be effective, which period shall not exceed twenty-seven (27) months beginning with the Offering Date, and the substance of the
provisions contained in Sections 5 through 8, inclusive. 
 (b) If a Participant has more than one
Purchase Right outstanding under the Plan, unless he or she otherwise indicates in agreements or notices delivered hereunder: (i) each agreement or notice delivered by that Participant shall be deemed to apply to all of his or her Purchase
Rights under the Plan, and (ii) a Purchase Right with a lower exercise price (or an earlier-granted Purchase Right, if different Purchase Rights have identical exercise prices) shall be exercised to the fullest possible extent before a Purchase
Right with a higher exercise price (or a later-granted Purchase Right if different Purchase Rights have identical exercise prices) shall be exercised. 
 (c) The Board shall have the discretion to structure an Offering so that if the Fair Market Value of the shares of Common Stock on the first day of a new Purchase Period within that Offering is
less than or equal to the Fair Market Value of the shares of Common Stock on the Offering Date, then (i) that Offering shall terminate immediately, and (ii) the Participants in such terminated Offering shall be automatically enrolled in a
new Offering beginning on the first day of such new Purchase Period. 
  

	5.	 ELIGIBILITY. 

 (a) Purchase Rights may be granted only to Employees of the Company or, as the Board may designate as provided in Section 2(b), to Employees of a Related Corporation. Except as provided in
Section 5(b), an Employee shall not be eligible to be granted Purchase Rights under the Plan unless, on the Offering Date, such Employee has been in the employ of the Company or the Related Corporation, as the case may be, for such continuous
period preceding such Offering Date as the Board may require, but in no event shall the required period of continuous employment be greater than two (2) years. In addition, the Board may provide that no Employee shall be eligible to be granted
Purchase Rights under the Plan unless, on the Offering Date, such Employee’s customary employment with the Company or the Related Corporation is more than twenty (20) hours per week and more than five (5) months per calendar year or
such other criteria as the Board may determine consistent with Section 423 of the Code. 
 (b) The
Board may provide that each person who, during the course of an Offering, first becomes an Eligible Employee shall, on a date or dates specified in the Offering which coincides with the day on which such person becomes an Eligible Employee or which
occurs thereafter, receive a Purchase Right under that Offering, which Purchase Right shall thereafter be deemed to be a part of that Offering. Such Purchase Right shall have the same characteristics as any Purchase Rights originally granted under
that Offering, as described herein, except that: 
  

 3. 

 (i) the date on which such Purchase Right is granted shall be the
“Offering Date” of such Purchase Right for all purposes, including determination of the exercise price of such Purchase Right; 
 (ii) the period of the Offering with respect to such Purchase Right shall begin on its Offering Date and end coincident with the end of such Offering; and 
 (iii) the Board may provide that if such person first becomes an Eligible Employee within a specified period of time
before the end of the Offering, he or she shall not receive any Purchase Right under that Offering. 
 (c) No Employee shall be eligible for the grant of any Purchase Rights under the Plan if, immediately after any such Purchase Rights are granted, such Employee owns stock possessing five percent (5%) or more of the total
combined voting power or value of all classes of stock of the Company or of any Related Corporation. For purposes of this Section 5(c), the rules of Section 424(d) of the Code shall apply in determining the stock ownership of any Employee,
and stock which such Employee may purchase under all outstanding Purchase Rights and options shall be treated as stock owned by such Employee. 
 (d) As specified by Section 423(b)(8) of the Code, an Eligible Employee may be granted Purchase Rights under the Plan only if such Purchase Rights, together with any other rights granted under
all Employee Stock Purchase Plans of the Company and any Related Corporations, do not permit such Eligible Employee’s rights to purchase stock of the Company or any Related Corporation to accrue at a rate which exceeds twenty five thousand
dollars ($25,000) of Fair Market Value of such stock (determined at the time such rights are granted, and which, with respect to the Plan, shall be determined as of their respective Offering Dates) for each calendar year in which such rights are
outstanding at any time. 
 (e) Officers of the Company and any designated Related Corporation, if they
are otherwise Eligible Employees, shall be eligible to participate in Offerings under the Plan. Notwithstanding the foregoing, the Board may provide in an Offering that Employees who are highly compensated Employees within the meaning of
Section 423(b)(4)(D) of the Code shall not be eligible to participate. 
  

	6.	 PURCHASE RIGHTS; PURCHASE PRICE. 

 (a) On each Offering Date, each Eligible Employee, pursuant to an Offering made under the Plan, shall be granted a
Purchase Right to purchase up to that number of shares of Common Stock purchasable either with a percentage or with a maximum dollar amount, as designated by the Board, but in either case not exceeding fifteen percent (15%) of such
Employee’s earnings (as defined by the Board in each Offering) during the period that begins on the Offering Date (or such later date as the Board determines for a particular Offering) and ends on the date stated in the Offering, which date
shall be no later than the end of the Offering. 
 (b) The Board shall establish one (1) or more
Purchase Dates during an Offering as of which Purchase Rights granted pursuant to that Offering shall be exercised and purchases of shares of Common Stock shall be carried out in accordance with such Offering. 
  

 4. 

 (c) In connection with each Offering made under the Plan, the Board
may specify a maximum number of shares of Common Stock that may be purchased by any Participant on any Purchase Date during such Offering. In connection with each Offering made under the Plan, the Board may specify a maximum aggregate number of
shares of Common Stock that may be purchased by all Participants pursuant to such Offering. In addition, in connection with each Offering that contains more than one Purchase Date, the Board may specify a maximum aggregate number of shares of Common
Stock that may be purchased by all Participants on any Purchase Date under the Offering. If the aggregate purchase of shares of Common Stock issuable upon exercise of Purchase Rights granted under the Offering would exceed any such maximum aggregate
number, then, in the absence of any Board action otherwise, a pro rata allocation of the shares of Common Stock available shall be made in as nearly a uniform manner as shall be practicable and equitable. 
 (d) The purchase price of shares of Common Stock acquired pursuant to Purchase Rights shall be not less than the
lesser of: 
 (i) an amount equal to eighty-five percent (85%) of the Fair Market Value of the
shares of Common Stock on the Offering Date; or 
 (ii) an amount equal to eighty-five percent
(85%) of the Fair Market Value of the shares of Common Stock on the applicable Purchase Date. 
  

	7.	 PARTICIPATION; WITHDRAWAL; TERMINATION. 

 (a) A Participant may elect to authorize payroll deductions pursuant to an Offering under the Plan by completing and
delivering to the Company, within the time specified in the Offering, an enrollment form (in such form as the Company may provide). Each such enrollment form shall authorize an amount of Contributions expressed as a percentage of the submitting
Participant’s earnings (as defined in each Offering) during the Offering (not to exceed the maximum percentage specified by the Board). Each Participant’s Contributions shall be credited to a bookkeeping account for such Participant under
the Plan and shall be deposited with the general funds of the Company except where applicable law requires that Contributions be deposited with a third party. To the extent provided in the Offering, a Participant may begin such Contributions after
the beginning of the Offering. To the extent provided in the Offering, a Participant may thereafter reduce (including to zero) or increase his or her Contributions. To the extent specifically provided in the Offering, in addition to making
Contributions by payroll deductions, a Participant may make Contributions through the payment by cash or check prior to each Purchase Date of the Offering. 
 (b) During an Offering, a Participant may cease making Contributions and withdraw from the Offering by delivering to the Company a notice of withdrawal in such form as the
Company may provide. Such withdrawal may be elected at any time prior to the end of the Offering, except as provided otherwise in the Offering. Upon such withdrawal from the Offering by a Participant, the Company shall distribute to such Participant
all of his or her accumulated Contributions (reduced to the extent, if any, such Contributions have been used to acquire shares of Common Stock for the Participant) under the Offering, and such Participant’s Purchase Right in that Offering
shall thereupon terminate. A Participant’s withdrawal from an Offering shall have no effect upon such Participant’s eligibility to participate in any other Offerings under the Plan, but such Participant shall be required to deliver a new
enrollment form in order to participate in subsequent Offerings. 
  

 5. 

 (c) Purchase Rights granted pursuant to any Offering under the Plan
shall terminate immediately upon a Participant ceasing to be an Employee for any reason or for no reason (subject to any post-employment participation period required by law) or other lack of eligibility. The Company shall distribute to such
terminated or otherwise ineligible Employee all of his or her accumulated Contributions (reduced to the extent, if any, such Contributions have been used to acquire shares of Common Stock for the terminated or otherwise ineligible Employee) under
the Offering. 
 (d) Purchase Rights shall not be transferable by a Participant except by will, the laws
of descent and distribution, or by a beneficiary designation as provided in Section 10. During a Participant’s lifetime, Purchase Rights shall be exercisable only by such Participant. 
 (e) Unless otherwise specified in an Offering, the Company shall have no obligation to pay interest on Contributions.

  

	8.	 EXERCISE OF PURCHASE RIGHTS. 

 (a) On each Purchase Date during an Offering, each Participant’s accumulated Contributions shall be applied to
the purchase of shares of Common Stock up to the maximum number of shares of Common Stock permitted pursuant to the terms of the Plan and the applicable Offering, at the purchase price specified in the Offering. No fractional shares shall be issued
upon the exercise of Purchase Rights unless specifically provided for in the Offering. 
 (b) If any
amount of accumulated Contributions remains in a Participant’s account after the purchase of shares of Common Stock and such remaining amount is less than the amount required to purchase one share of Common Stock on the final Purchase Date of
an Offering, then such remaining amount shall be held in such Participant’s account for the purchase of shares of Common Stock under the next Offering under the Plan, unless such Participant withdraws from such next Offering, as provided in
Section 7(b), or is not eligible to participate in such Offering, as provided in Section 5, in which case such amount shall be distributed to such Participant after the final Purchase Date, without interest. If the amount of Contributions
remaining in a Participant’s account after the purchase of shares of Common Stock is at least equal to the amount required to purchase one (1) whole share of Common Stock on the final Purchase Date of the Offering, then such remaining
amount shall be distributed in full to such Participant at the end of the Offering without interest. 
 (c) No Purchase Rights may be exercised to any extent unless the shares of Common Stock to be issued upon such exercise under the Plan are covered by an effective registration statement pursuant to the Securities Act and the Plan is
in material compliance with all applicable federal, state, foreign and other securities and other laws applicable to the Plan. If on a Purchase Date during any Offering hereunder the shares of Common Stock are not so registered or the Plan is not in
such compliance, no Purchase Rights or any Offering shall be exercised on such Purchase Date, and the Purchase Date shall be delayed until the shares of Common Stock are subject to such an effective registration statement and the Plan is in such
compliance, except that the Purchase Date shall not be delayed more than twelve (12) months and the Purchase Date shall in no event be more than twenty-seven (27) months from the Offering Date. If, on the Purchase Date under any Offering
hereunder, as delayed to the maximum extent permissible, the shares of Common Stock are not registered and the Plan is not in such compliance, no Purchase Rights or any Offering shall be exercised and all Contributions accumulated during the
Offering (reduced to the extent, if any, such Contributions have been used to acquire shares of Common Stock) shall be distributed to the Participants without interest. 
  

 6. 

	9.	 COVENANTS OF THE COMPANY. 

 The Company shall seek to obtain from each federal, state, foreign or other regulatory commission or agency having
jurisdiction over the Plan such authority as may be required to issue and sell shares of Common Stock upon exercise of the Purchase Rights. If, after commercially reasonable efforts, the Company is unable to obtain from any such regulatory
commission or agency the authority that counsel for the Company deems necessary for the lawful issuance and sale of Common Stock under the Plan, the Company shall be relieved from any liability for failure to issue and sell Common Stock upon
exercise of such Purchase Rights unless and until such authority is obtained. 
  

	10.	 DESIGNATION OF BENEFICIARY. 

 (a) A Participant may file a written designation of a beneficiary who is to receive any shares of Common Stock and/or
cash, if any, from the Participant’s account under the Plan in the event of such Participant’s death subsequent to the end of an Offering but prior to delivery to the Participant of such shares of Common Stock or cash. In addition, a
Participant may file a written designation of a beneficiary who is to receive any cash from the Participant’s account under the Plan in the event of such Participant’s death during an Offering. Any such designation shall be on a form
provided by or otherwise acceptable to the Company. 
 (b) The Participant may change such designation of
beneficiary at any time by written notice to the Company. In the event of the death of a Participant and in the absence of a beneficiary validly designated under the Plan who is living at the time of such Participant’s death, the Company shall
deliver such shares of Common Stock and/or cash to the executor or administrator of the estate of the Participant, or if no such executor or administrator has been appointed (to the knowledge of the Company), the Company, in its sole discretion, may
deliver such shares of Common Stock and/or cash to the spouse or to any one or more dependents or relatives of the Participant, or if no spouse, dependent or relative is known to the Company, then to such other person as the Company may designate.

  

	11.	 ADJUSTMENTS UPON CHANGES IN COMMON STOCK;
CORPORATE TRANSACTIONS. 

 (a) In the event of a
Capitalization Adjustment, the Board shall appropriately and proportionately adjust: (i) the class(es) and maximum number of securities subject to the Plan pursuant to Section 3(a), (ii) the class(es) and maximum number of securities
by which the share reserve is to increase automatically each year pursuant to Section 3(a), (iii) the class(es) and number of securities subject to, and the purchase price applicable to outstanding Offerings and Purchase Rights, and
(iv) the class(es) and number of securities imposed by purchase limits under each ongoing Offering. The Board shall make such adjustments, and its determination shall be final, binding and conclusive. 
  

 7. 

 (b) In the event of a Corporate Transaction, then: (i) any
surviving corporation or acquiring corporation (or the surviving or acquiring corporation’s parent company) may assume or continue Purchase Rights outstanding under the Plan or may substitute similar rights (including a right to acquire the
same consideration paid to the stockholders in the Corporate Transaction) for those outstanding under the Plan, or (ii) if any surviving or acquiring corporation (or its parent company) does not assume or continue such Purchase Rights or does
not substitute similar rights for Purchase Rights outstanding under the Plan, then the Participants’ accumulated Contributions shall be used to purchase shares of Common Stock within ten (10) business days prior to the Corporate
Transaction under any ongoing Offerings, and the Participants’ Purchase Rights under the ongoing Offerings shall terminate immediately after such purchase. 
  

	12.	 AMENDMENT, TERMINATION OR SUSPENSION OF THE
PLAN. 

 (a) The Board may amend the Plan at any time in any respect
the Board deems necessary or advisable. However, except as provided in Section 11(a) relating to Capitalization Adjustments, stockholder approval shall be required for any amendment of the Plan for which stockholder approval is required by
applicable law or listing requirements, including any amendment that either (i) materially increases the number of shares of Common Stock available for issuance under the Plan, (ii) materially expands the class of individuals eligible to
become Participants and receive Purchase Rights under the Plan, (iii) materially increases the benefits accruing to Participants under the Plan or materially reduces the price at which shares of Common Stock may be purchased under the Plan,
(iv) materially extends the term of the Plan, or (v) expands the types of awards available for issuance under the Plan, but in each of (i) through (v) above only to the extent stockholder approval is required by applicable law or
listing requirements. 
 (b) The Board may suspend or terminate the Plan at any time. No Purchase Rights
may be granted under the Plan while the Plan is suspended or after it is terminated. 
 (c) Any benefits,
privileges, entitlements and obligations under any outstanding Purchase Rights granted before an amendment, suspension or termination of the Plan shall not be impaired by any such amendment, suspension or termination except (i) with the consent
of the person to whom such Purchase Rights were granted, (ii) as necessary to comply with any laws, listing requirements, or governmental regulations (including, without limitation, the provisions of Section 423 of the Code and the
regulations and other interpretive guidance issued thereunder relating to Employee Stock Purchase Plans) including without limitation any such regulations or other guidance that may be issued or amended after the Effective Date, or (iii) as
necessary to obtain or maintain favorable tax, listing, or regulatory treatment. 
  

 8. 

	13.	 EFFECTIVE DATE OF PLAN. 

 The Plan shall become effective on the IPO Date, but no Purchase Rights shall be exercised unless and until the Plan has been
approved by the stockholders of the Company, which approval shall be within twelve (12) months before or after the date the Plan is adopted by the Board. 
  

	14.	 MISCELLANEOUS PROVISIONS. 

 (a) Proceeds from the sale of shares of Common Stock pursuant to Purchase Rights shall constitute general funds of the
Company. 
 (b) A Participant shall not be deemed to be the holder of, or to have any of the rights of a
holder with respect to, shares of Common Stock subject to Purchase Rights unless and until the Participant’s shares of Common Stock acquired upon exercise of Purchase Rights are recorded in the books of the Company (or its transfer agent).

 (c) The Plan and Offering do not constitute an employment contract. Nothing in the Plan or in the
Offering shall in any way alter the at will nature of a Participant’s employment or be deemed to create in any way whatsoever any obligation on the part of any Participant to continue in the employ of the Company or a Related Corporation, or on
the part of the Company or a Related Corporation to continue the employment of a Participant. 
 (d) The
provisions of the Plan shall be governed by the laws of the state of California without resort to that state’s conflicts of laws rules. 
  

	15.	 DEFINITIONS. 

 As used in the Plan, the following definitions shall apply to the capitalized terms indicated below: 
 (a) “Board” means the Board of Directors of the Company. 
 (b) “Capitalization Adjustment” means any change that is made in, or other events that occur with respect to, the Common Stock subject to the Plan or subject to any Purchase
Right after the Effective Date without the receipt of consideration by the Company (through merger, consolidation, reorganization, recapitalization, reincorporation, stock dividend, dividend in property other than cash, stock split, liquidating
dividend, combination of shares, exchange of shares, change in corporate structure or other similar transaction). Notwithstanding the foregoing, the conversion of any convertible securities of the Company shall not be treated as a Capitalization
Adjustment. 
 (c) “Code” means the Internal Revenue Code of 1986, as amended,
including any applicable regulations and guidance thereunder. 
 (d) “Committee”
means a committee of one (1) or more members of the Board to whom authority has been delegated by the Board in accordance with Section 2(c). 
  

 9. 

 (e) “Common Stock” means the common stock of
the Company. 
 (f) “Company” means Trius Therapeutics, Inc., a Delaware
corporation. 
 (g) “Contributions” means the payroll deductions and other
additional payments specifically provided for in the Offering, that a Participant contributes to fund the exercise of a Purchase Right. A Participant may make additional payments into his or her account, if specifically provided for in the Offering,
and then only if the Participant has not already had the maximum permitted amount withheld during the Offering through payroll deductions. 
 (h) “Corporate Transaction” means the occurrence, in a single transaction or in a series of related transactions, of any one or more of the following events: 
 (i) the consummation of a sale or other disposition of all or substantially all, as determined by the Board in its
sole discretion, of the consolidated assets of the Company and its Subsidiaries; 
 (ii) the consummation
of a sale or other disposition of at least ninety percent (90%) of the outstanding securities of the Company; 
 (iii) the consummation of a merger, consolidation or similar transaction following which the Company is not the surviving corporation; or 
 (iv) the consummation of a merger, consolidation or similar transaction following which the Company is the surviving corporation but the shares of Common Stock outstanding immediately preceding the
merger, consolidation or similar transaction are converted or exchanged by virtue of the merger, consolidation or similar transaction into other property, whether in the form of securities, cash or otherwise. 
 (i) “Director” means a member of the Board. 
 (j) “Eligible Employee” means an Employee who meets the requirements set forth in the
Offering for eligibility to participate in the Offering, provided that such Employee also meets the requirements for eligibility to participate set forth in the Plan. 
 (k) “Employee” means any person, including Officers and Directors, who is employed for purposes of Section 423(b)(4) of the Code by the Company or
a Related Corporation. However, service solely as a Director, or payment of a fee for such services, shall not cause a Director to be considered an “Employee” for purposes of the Plan. 
 (l) “Employee Stock Purchase Plan” means a plan that grants Purchase Rights intended to be
options issued under an “employee stock purchase plan,” as that term is defined in Section 423(b) of the Code. 
 (m) “Exchange Act” means the Securities Exchange Act of 1934, as amended, and the rules and regulations promulgated thereunder. 
  

 10. 

 (n) “Fair Market Value” means, as of any
date, the value of the Common Stock determined as follows: 
 (i) If the Common Stock is listed on any
established stock exchange or traded on any established market, the Fair Market Value of a share of Common Stock shall be the closing sales price for such stock as quoted on such exchange or market (or the exchange or market with the greatest volume
of trading in the Common Stock) on the date of determination, as reported in a source the Board deems reliable. Unless otherwise provided by the Board, if there is no closing sales price for the Common Stock on the date of determination, then the
Fair Market Value shall be the closing selling price on the last preceding date for which such quotation exists. 
 (ii) In the absence of such markets for the Common Stock, the Fair Market Value shall be determined by the Board in good faith and in a manner that complies with Sections 409A of the Code. 
 (iii) Notwithstanding the foregoing, for any Offering that commences on the IPO Date, the Fair Market Value of the
shares of Common Stock at the time when the Offering commences shall be the price per share at which shares are first sold to the public in the Company’s initial public offering as specified in the final prospectus for that initial public
offering. 
 (o) “IPO Date” means the date of the underwriting agreement between
the Company and the underwriter(s) managing the initial public offering of the Common Stock, pursuant to which the Common Stock is priced for the initial public offering. 
 (p) “Offering” means the grant of Purchase Rights to purchase shares of Common Stock under the Plan to Eligible Employees. 
 (q) “Offering Date” means a date selected by the Board for an Offering to commence.

 (r) “Officer” means a person who is an officer of the Company within the
meaning of Section 16 of the Exchange Act. 
 (s) “Participant” means an
Eligible Employee who holds an outstanding Purchase Right granted pursuant to the Plan. 
 (t)
“Plan” means this Trius Therapeutics, Inc. 2010 Employee Stock Purchase Plan. 
 (u) “Purchase Date” means one or more dates during an Offering established by the Board on which Purchase Rights shall be exercised and as of which purchases of shares of Common Stock shall be carried out in
accordance with such Offering. 
 (v) “Purchase Period” means a period of time
specified within an Offering beginning on the Offering Date or on the next day following a Purchase Date within an Offering and ending on a Purchase Date. An Offering may consist of one or more Purchase Periods. 
  

 11. 

 (w) “Purchase Right” means an option to
purchase shares of Common Stock granted pursuant to the Plan. 
 (x) “Related
Corporation” means any “parent corporation” or “subsidiary corporation” of the Company whether now or subsequently established, as those terms are defined in Sections 424(e) and (f), respectively, of the Code.

 (y) “Securities Act” means the Securities Act of 1933, as amended. 

(z) “Trading Day” means any day on which the exchange(s) or market(s) on which shares of
Common Stock are listed, including the Nasdaq Global Select Market, the Nasdaq Global Market, or the Nasdaq Capital Market, is open for trading. 
  

 12. 

 TRIUS THERAPEUTICS, INC. 
 2010 EMPLOYEE STOCK PURCHASE PLAN 
 OFFERING DOCUMENT 
 ADOPTED BY THE BOARD OF DIRECTORS:
[                    ], 2010 
 In this document, capitalized terms not otherwise defined shall have the same definitions of such terms as in the Trius Therapeutics, Inc. 2010 Employee Stock Purchase Plan. 
  

	1.	 GRANT; OFFERING DATE. 

 (a) The Board hereby authorizes a series of Offerings pursuant to the terms of this Offering document. 
 (b) The first Offering hereunder (the “Initial Offering”) shall begin on the IPO Date and
shall end approximately 24 months following the commencement of the Initial Offering, unless terminated earlier as provided below. The Initial Offering shall consist of four (4) Purchase Periods, approximately six (6) months in length
ending on or about                          and
                         each year with the first Purchase Period ending on
                        , the second Purchase Period ending on
                        , the third Purchase Period ending on
                        , and the fourth Purchase Period ending on
                        . 
 (c) After the Initial Offering ends, a new Offering shall automatically begin over the term of the Plan on the day after the last Purchase Date of the immediately preceding Offering, and each new
Offering shall be approximately twenty-four (24) months in duration. Each Offering shall consist of four (4) Purchase Periods approximately six (6) months in length ending on or about
                         and
                         each year. Except as provided below, a Purchase Date is the last day of a Purchase Period or of
an Offering, as the case may be. 
 (d) Notwithstanding the foregoing: (i) if any Offering Date
falls on a day that is not a Trading Day, then such Offering Date shall instead fall on the next subsequent Trading Day, and (ii) if any Purchase Date falls on a day that is not a Trading Day, then such Purchase Date shall instead fall on the
immediately preceding Trading Day. 
 (e) Prior to the commencement of any Offering, the Board may change
any or all terms of such Offering and any subsequent Offerings. The granting of Purchase Rights pursuant to each Offering hereunder shall occur on each respective Offering Date unless prior to such date (i) the Board determines that such
Offering shall not occur, or (ii) no shares of Common Stock remain available for issuance under the Plan in connection with the Offering. 
 (f) Notwithstanding anything in this Section 1 to the contrary, if the Fair Market Value of a share of Common Stock on any Purchase Date during an Offering is less than or equal to the Fair
Market Value of a share of Common Stock on the Offering Date for that Offering, then that Offering shall terminate immediately following the purchase of shares of Common Stock on such Purchase Date. Participants in the terminated Offering
automatically shall be enrolled in the Offering that commences immediately after such Purchase Date. Thereafter, notwithstanding the provisions of Section 1(c) above, instead of a new Offering commencing pursuant to Section 1(c), a new
Offering shall begin on the 24-month anniversary of the new Offering that commences pursuant to this Section 1(f) and every 24 months thereafter, and each such Offering shall end on the day prior to the 24-month anniversary of its Offering
Date. It is intended that Sections 1(c) and 1(f) shall operate so that only one Offering shall be outstanding at any time under the Plan, and that at all times one Offering shall be outstanding under the Plan. 
  

 1. 

	2.	 ELIGIBLE EMPLOYEES. 

 (a) Each Eligible Employee, who is either (i) an employee of the Company or (ii) an employee of a Related Corporation incorporated in the United States, provided
that the Board or Committee has designated the employees of such Related Corporation as eligible to participate in the Offering, shall be granted a Purchase Right on the Offering Date of such Offering. 
 (b) Each person who, during the course of an Offering, first becomes an Eligible Employee prior to the commencement
of the last Purchase Period under the Offering shall, on the first Trading Day of the first Purchase Period that commences after such person becomes an Eligible Employee, receive a Purchase Right under that Offering, which Purchase Right shall
thereafter be deemed to be a part of that Offering; provided, however, that such Eligible Employee submits the necessary enrollment paperwork required by the Company on or before such date. Such Purchase Right shall have the same
characteristics as any Purchase Rights originally granted under that Offering, as described herein, except that: 
 (i) the date on which such Purchase Right is granted shall be the “Offering Date” of such Purchase Right for all purposes, including determination of the exercise price of such Purchase Right except for the application of
the provision of Section 1(f) above (the application of which shall be determined only by using the Offering Date of the ongoing Offering that is the first day of the Offering), including determination of the exercise price of such Purchase
Right; and 
 (ii) the period of the Offering with respect to such Purchase Right shall begin on its
Offering Date and end coincident with the end of such Offering. 
 (c) Notwithstanding the foregoing, the
following Employees shall not be Eligible Employees or be granted Purchase Rights under an Offering: 
 (i) five percent (5%) stockholders (including ownership through unexercised and/or unvested stock options) as described in Section 5(c) of the Plan; or 
 (ii) Employees in jurisdictions outside of the United States. 
  

	3.	 PURCHASE RIGHTS. 

 (a) Subject to the limitations herein and in the Plan, a Participant’s Purchase Right shall permit the purchase of the number of shares of Common Stock purchasable with
up to fifteen percent (15%) of such Participant’s Earnings paid during the period of such Offering beginning immediately after such Participant first commences participation; provided, however, that no Participant may have more than
fifteen percent (15%) of such Participant’s Earnings applied to purchase shares of Common Stock under all ongoing Offerings under the Plan and all other plans of the Company and Related Corporations that are intended to qualify as Employee
Stock Purchase Plans. 
  

 2. 

 (b) For Offerings hereunder, “Earnings” means
the base compensation paid to a Participant, including all salary, wages (including amounts elected to be deferred by such Participant, that would otherwise have been paid, under any cash or deferred arrangement or other deferred compensation
program established by the Company or a Related Corporation), but excluding all of the following: all overtime pay, commissions, bonuses, and other remuneration paid directly to such Participant, profit sharing, the cost of employee benefits paid
for by the Company or a Related Corporation, education or tuition reimbursements, imputed income arising under any Company or Related Corporation group insurance or benefit program, traveling expenses, business and moving expense reimbursements,
income received in connection with stock options and other equity awards, contributions made by the Company or a Related Corporation under any employee benefit plan, and other similar items of compensation. 
 (c) Notwithstanding the foregoing, the maximum number of shares of Common Stock that a Participant may purchase on
any Purchase Date in an Offering shall be such number of shares as has a Fair Market Value (determined as of the Offering Date for such Offering) equal to (x) $25,000 multiplied by the number of calendar years in which the Purchase Right under
such Offering has been outstanding at any time, minus (y) the Fair Market Value of any other shares of Common Stock (determined as of the relevant Offering Date with respect to such shares) that, for purposes of the limitation of
Section 423(b)(8) of the Code, are attributed to any of such calendar years in which the Purchase Right is outstanding. The amount in clause (y) of the previous sentence shall be determined in accordance with regulations applicable under
Section 423(b)(8) of the Code based on (i) the number of shares previously purchased with respect to such calendar years pursuant to such Offering or any other Offering under the Plan, or pursuant to any other Company or Related
Corporation plans intended to qualify as Employee Stock Purchase Plans, and (ii) the number of shares subject to other Purchase Rights outstanding on the Offering Date for such Offering pursuant to the Plan or any other such Company or Related
Corporation Employee Stock Purchase Plan. 
 (d) The maximum aggregate number of shares of Common Stock
available to be purchased by all Participants under an Offering shall be the number of shares of Common Stock remaining available under the Plan on the Offering Date, rounded down to the nearest whole share. If the aggregate purchase of shares of
Common Stock upon exercise of Purchase Rights granted under the Offering would exceed the maximum aggregate number of shares available, the Board shall make a pro rata allocation of the shares available in a uniform and equitable manner. Any
Contributions not applied to the purchase of available shares of Common Stock shall be refunded to the Participants without interest. 
 (e) Notwithstanding the foregoing, the maximum number of shares of Common Stock that may be purchased on any single Purchase Date by all Eligible Employees during any Offering shall not exceed
[                ] shares. 
  

 3. 

 (f) If the aggregate number of shares of Common Stock to be purchased
upon the exercise of all outstanding Purchase Rights on a single Purchase Date would exceed any of the foregoing limits, the Board shall make a uniform and equitable allocation of the shares available. Any Contributions not applied to the purchase
of available shares of Common Stock shall be refunded to the Participants without interest. 
  

	4.	 PURCHASE PRICE. 

 The purchase price of shares of Common Stock under an Offering shall be the lesser of: (i) eighty-five percent (85%) of the Fair Market Value of such shares of Common Stock
on the Offering Date, or (ii) eighty-five percent (85%) of the Fair Market Value of such shares of Common Stock on the applicable Purchase Date, in each case rounded up to the nearest whole cent per share. For the Initial Offering, the
Fair Market Value of the shares of Common Stock at the time when the Offering commences shall be the price per share at which shares are first sold to the public in the Company’s initial public offering as specified in the final prospectus for
that initial public offering. 
  

	5.	 PARTICIPATION. 

 (a) An Eligible Employee may elect to participate in an Offering to be effective on the Offering Date. An Eligible Employee shall elect his or her payroll deduction percentage on such enrollment
form as the Company provides. The completed enrollment form must be delivered to the Company at least ten (10) days prior to the date participation is to be effective, unless a later time for filing the enrollment form is set by the Company for
all Eligible Employees with respect to a given Offering. Payroll deduction percentages must be expressed in whole percentages of Earnings, with a minimum percentage of one percent (1%) and a maximum percentage of fifteen percent (15%). Except
as provided in Section 5(g), a Participant may participate only by way of payroll deductions. 
 (b)
A Participant may increase or decrease his or her participation level at any time with such change to be effective commencing as of the next Offering. Any such increase or decrease in participation level shall be made by delivering a notice to the
Company or a designated Related Corporation in such form as the Company provides prior to the ten (10) day period (or such shorter period of time as determined by the Company and communicated to Participants) immediately preceding the next
Offering Date for which it is to be effective. A Participant may also increase or decrease his or her participation level to be effective in a subsequent Purchase Period of an ongoing Offering in accordance with procedures established by the
Company. 
 (c) A Participant may increase his or her participation level once during a Purchase Period.
In addition, a Participant may decrease (including a decrease to zero percent (0%)) his or her participation level no more than once during a Purchase Period. Any such change in participation level shall be made by delivering a notice to the Company
or a designated Related Corporation in such form as the Company provides prior to the ten (10) day period (or such shorter period of time as determined by the Company and communicated to Participants) immediately preceding the payroll date for
which it is to be effective and such change will become                     

  

 4. 

 
effective as soon as administratively practicable following the Company’s receipt of the notice. Any Participant who has not increased his or her payroll deduction level from zero percent
(0%) to at least one percent (1%) by the time proscribed before the start of a new Offering shall be deemed to have withdrawn from the Plan effective as of, respectively, the first day of that new Offering. 
 (d) A Participant may withdraw from an Offering and receive a refund of his or her Contributions (reduced to the
extent, if any, such Contributions have been used to acquire shares of Common Stock for the Participant on any prior Purchase Date) without interest, at any time prior to the end of the Offering, excluding only each ten (10) day period
immediately preceding a Purchase Date (or such shorter period of time determined by the Company and communicated to Participants), by delivering a withdrawal notice to the Company or a designated Related Corporation in such form as the Company
provides. A Participant who has withdrawn from an Offering shall not again participate in such Offering, but may participate in subsequent Offerings under the Plan in accordance with the terms of the Plan and the terms of such subsequent Offerings.

 (e) Notwithstanding the foregoing or any other provision of this Offering document or of the Plan to
the contrary, neither the enrollment of any Eligible Employee in the Plan nor any forms relating to participation in the Plan shall be given effect until such time as a registration statement covering the shares reserved under the Plan that are
subject to the Offering has been filed by the Company and has become effective. If the provisions of this Section are applicable, the Company shall establish such procedures as will enable the purposes of the Plan to be satisfied while complying
with applicable securities laws. Such procedures may include, for example, allowing Participants to participate other than by means of payroll deduction and/or allowing Participants to increase their level of participation during a Purchase Period.

 (f) Notwithstanding the foregoing or any other provision of this Offering document or of the Plan to
the contrary, the Company may determine in its sole discretion at any time, including at any time following the commencement of an Offering or Purchase Period, that it will no longer accept Participant requests to increase participation levels
during such Offering or Purchase Period, as applicable. 
 (g) Notwithstanding the foregoing or any other
provision of this Offering document or of the Plan to the contrary, with respect to the Initial Offering only, each Eligible Employee who is employed on the Offering Date for the Initial Offering automatically shall be enrolled in the Initial
Offering, with a Purchase Right to purchase up to the number of shares of Common Stock that are purchasable with fifteen percent (15%) of the Eligible Employee’s Earnings, subject to the limitations set forth in Section 3(c)—3(f)
above. Following the filing of an effective registration statement pursuant to a Form S-8, such Eligible Employee shall be provided a certain period of time, as determined by the Company in its sole discretion, within which to elect to authorize
payroll deductions for the purchase of shares during the Initial Offering (which may be for a percentage that is less than fifteen percent (15%) of the Eligible Employee’s Earnings, and will have a limited opportunity to make all or part
of the contributions in a single lump sum cash payment for the purchase of such shares to the Company or a designated Related Corporation prior to the ten (10) day period (or such shorter period of time as determined by the Company and
communicated to Participants) immediately preceding the first Purchase Date                  
  

 5. 

 
under the Initial Offering. To the extent that the Eligible Employee’s payroll deductions for such initial Purchase Period are less than fifteen percent (15%) of the Eligible
Employee’s Earnings paid to the Eligible Employee during the initial Purchase Period of the Offering, the Eligible Employee may make an additional cash payment at any time or prior to the ten (10) day period (or such shorter period of time
as determined by the Company and communicated to Participants) immediately preceding the Purchase Date under the Initial Offering. If an Eligible Employee neither elects to authorize payroll deductions nor chooses to make a cash payment in
accordance with the foregoing sentence, then the Eligible Employee shall not purchase any shares of Common Stock during the Initial Offering. In order to participate in any Offerings that follow the Initial Offering, an Eligible Employee must
affirmatively enroll and authorize payroll deductions prior to the commencement of the Offering, in accordance with paragraph (a) above. 
 (h) Once an Eligible Employee affirmatively enrolls in an Offering and authorizes payroll deductions (including in connection with the Initial Offering), the Eligible Employee automatically shall
be enrolled for all subsequent Offerings until he or she elects to withdraw from an Offering pursuant to paragraph (d) above or terminates his or her participation in the Plan. 
  

	6.	 PURCHASES. 

 Subject to the limitations contained herein, on each Purchase Date, each Participant’s Contributions (without any increase for interest) shall be applied to the purchase of whole shares of Common
Stock, up to the maximum number of shares permitted under the Plan and the Offering. 
  

	7.	 NOTICES AND AGREEMENTS. 

 Any notices or agreements provided for in an Offering or the Plan shall be given in writing, in a form provided by the
Company (including documents delivered in electronic form, if authorized by the Committee), and unless specifically provided for in the Plan or this Offering, shall be deemed effectively given upon receipt or, in the case of notices and agreements
delivered by the Company, five (5) days after deposit in the United States mail, postage prepaid. 
  

	8.	 EXERCISE CONTINGENT ON STOCKHOLDER APPROVAL.

 The Purchase Rights granted under an Offering are subject to the approval of the Plan by
the stockholders of the Company as required for the Plan to obtain treatment as an Employee Stock Purchase Plan. 
  

	9.	 CAPITALIZATION ADJUSTMENTS. 

 The limitation set forth in Section 3(e) shall be adjusted, as appropriate, to reflect Capitalization Adjustments.

  

	10.	 OFFERING SUBJECT TO PLAN. 

 Each Offering is subject to all the provisions of the Plan, and the provisions of the Plan are hereby made a part of the
Offering. The Offering is further subject to all interpretations, amendments, rules and regulations which may from time to time be promulgated             

  

 6. 

 
and adopted pursuant to the Plan. In the event of any conflict between the provisions of an Offering and those of the Plan (including interpretations, amendments, rules and regulations which may
from time to time be promulgated and adopted pursuant to the Plan), the provisions of the Plan shall control. 
  

 7.Employment Agreement

 Exhibit 10.6 
 EMPLOYMENT AGREEMENT 
 This
EMPLOYMENT AGREEMENT (the “Agreement”) is made and entered into effective as of February 1, 2007 (the “Effective Date”), by and between TRIUS
THERAPEUTICS, INC. (the “Company”), and JEFFREY STEIN (the “Executive”). The Company and the Executive may be hereinafter collectively referred
to as the “Parties”, and individually referred to as a “Party”. 
 A.
The Company desires assurance of the association and services of the Executive in order to retain the Executive’s experience, skills, abilities, background and knowledge, and is willing to engage the Executive’s services on the terms
and conditions set forth in this Agreement. 
 B. The Executive desires to be in the employ of the
Company, and is willing to accept such employment on the terms and conditions set forth in this Agreement. 
 AGREEMENT 
 In consideration of the foregoing recitals and the mutual promises
and covenants herein contained, and for other good and valuable consideration, the Parties, intending to be legally bound, agree as follows: 
  

	 	1.	 EMPLOYMENT. 

 1.1 Employment At Will. The Company hereby employs the Executive, and the Executive hereby accepts employment by the Company, upon the terms and conditions set forth in this
Agreement. The Executive’s employment with the Company shall be at will. Either the Executive or the Company may terminate the employment relationship at any time and for any reason, with or without cause or prior notice. 
 1.2 Termination of Consulting Agreement. The Parties agree that the Consulting Agreement between the
Executive and the Company, dated June 1, 2005 (the “Consulting Agreement”), shall terminate immediately upon the Effective Date of this Agreement and shall have no further force or effect. In exchange for the consideration to
be paid to the Executive under this Agreement, which he is not otherwise entitled to receive, the Executive hereby waives the right to any compensation or benefits he may have been entitled to under the Consulting Agreement, including but not
limited to bonuses and consulting fees (other than payment by the Company of $62,500 in accrued fees to the Executive pursuant to the Consulting Agreement). 
 1.3 Title. The Executive shall have the title of “President and Chief Executive Officer” and may also serve in such other capacity or capacities as the
Company’s Board of Directors (the “Board”) may from time to time prescribe. The Executive shall report to the Board. 

 1.4 Duties. The Executive shall do and perform all
services, acts and things reasonably necessary or advisable to manage and conduct the business of the Company and that are normally associated with the position of President and Chief Executive Officer, as well as any other services, acts and things
as may be reasonably required from time to time by the Board. 
 1.5 Location. Unless the
Parties otherwise agree in writing, the Executive shall perform services pursuant to this Agreement at the Company’s offices located in San Diego, California, or, with the Parties’ consent, at any other place where the Company maintains an
office, provided, however, that the Company may from time to time require the Executive to travel temporarily to other locations in connection with the Company’s business. 
 1.6 Policies and Practices. The employment relationship between the Parties shall be governed by this
Agreement along with the policies and practices established by the Company and the Board. In the event that the terms of this Agreement differ from or are in conflict with the Company’s policies or practices or the Company’s Employee
Handbook, this Agreement shall control. 
  

	 	2.	 LOYAL AND CONSCIENTIOUS PERFORMANCE; NONCOMPETITION.

 2.1 Loyalty. During the Executive’s employment by the Company,
the Executive shall devote the Executive’s full business energies, interest, abilities and productive time to the proper and efficient performance of the Executive’s duties under this Agreement. 
 2.2 Covenant not to Compete. Subject to Section 2.4, except with the prior written consent of the
Board, which consent shall not be unreasonably conditioned, delayed or withheld, the Executive will not, during his employment with the Company engage in competition with the Company and/or any of its Affiliates, either directly or indirectly, in
any manner or capacity, as adviser, principal, agent, affiliate, promoter, partner, officer, director, employee, stockholder, owner, co-owner, consultant, or member of any association or otherwise, in any phase of the business of developing,
manufacturing or marketing of products or services that are in the same field of use or which otherwise compete with the products or services or proposed products or services of the Company and/or any of its Affiliates. For purposes of this
Agreement, “Affiliate” means, with respect to any specific entity, any other entity that, directly or indirectly, through one or more intermediaries, controls, is controlled by or is under common control with such specified entity.

 2.3 Agreement not to Participate in Company’s Competitors. Subject to
Section 2.4, during his employment with the Company, the Executive agrees not to acquire, assume or participate in, directly or indirectly, any position, investment or interest known by Executive to be adverse or antagonistic to the Company,
its business, or prospects, financial or otherwise, or in any company, person, or entity that is, directly or indirectly, in competition with the business of the Company or any of its Affiliates.

  

 2. 

 
Ownership by the Executive, as a passive investment, of less than two percent (2%) of the outstanding shares of capital stock of any corporation with one or more classes of its capital stock
listed on a national securities exchange or publicly traded on the Nasdaq Stock Market or in the over-the-counter market shall not constitute a breach of this paragraph. 
 2.4 Permitted Activities. Notwithstanding the foregoing, nothing in this Agreement shall prohibit the
Executive from: (i) continuing in his role as a venture partner with Sofinnova Ventures, Inc. (together with its Affiliates, “Sofinnova”) and, to that end and without limitation, evaluating potential investments for Sofinnova,
serving on the board of directors of up to two (2) portfolio companies of Sofinnova (in addition to the Company) and participating in such other activities as required by Sofinnova of its venture partners, or (ii) completing the
Executive’s existing consulting engagement with Cadence Pharmaceuticals, Inc. 
  

	 	3.	 COMPENSATION OF THE EXECUTIVE. 

 3.1 Base Salary. The Company shall pay the Executive a base salary of two hundred seventy-five
thousand dollars ($275,000) per year, less any required withholdings and deductions, payable in regular periodic payments in accordance with Company policy (the “Base Salary”). Such Base Salary shall be prorated for any partial year
of employment on the basis of a 365-day fiscal year. 
 3.2 Discretionary Bonus. In
addition to the Executive’s Base Salary, the Executive shall also be eligible to receive an annual discretionary bonus. Whether the Executive shall receive a bonus in any given year and the amount of any such bonus shall be determined in the
sole and absolute discretion of the Board. 
 3.3 Stock Options. Subject to approval of
the Board and the terms of the Company’s Amended and Restated 2006 Equity Incentive Plan, as may be amended from time to time (the “Plan”), the Executive will be granted a stock option under the Plan to purchase 2,205,000
shares of the Company’s Common Stock (the “Option”). To the maximum extent possible, the Option shall be an Incentive Stock Option as such term is defined in Section 422 of the Internal Revenue Code of 1986, as amended.
The Option will be governed by and granted pursuant to a separate Stock Option Agreement and the Plan. The exercise price per share of the Option will be equal to the fair market value of a share of common stock on the grant date, which will be the
later of the date the Executive commences employment with the Company or the date that the Board approves the Option. Subject to the provisions of Section 4 below, the Option will be subject to vesting in thirty-six (36) equal and
consecutive monthly installments starting from the date the Executive commences employment with the Company and for so long as the Executive continues to be employed by the Company such that the Executive shall be vested in full in the Option
following three (3) full years of employment with the Company. 
 3.4 Changes to
Compensation. The Executive’s compensation may be changed from time to time in the Company’s discretion; provided, however, that the Executive’s compensation may not be decreased in any way without the Executive’s prior
written consent. 
  

 3. 

 3.5 Employment Taxes. All of the Executive’s
compensation shall be subject to withholding taxes and any other employment taxes as required by applicable law. 
 3.6 Health Benefits. The Company shall provide the Executive with health insurance coverage consistent with such coverage as is generally provided to similarly situated employees of the Company.

 3.7 Expense Reimbursements. The Executive shall be entitled to be reimbursed for all
reasonable business expenses incurred in connection with carrying on the Executive’s duties hereunder in accordance with the Company’s expense reimbursement policies. 
  

	 	4.	 TERMINATION. 

 4.1 Termination for Cause or Termination by the Executive. If the Executive’s employment is terminated by the Company for Cause (as defined below), or if the Executive
voluntarily terminates employment hereunder, the Company shall pay the Executive all Base Salary and accrued but unused vacation benefits earned through the date of termination at the rate in effect at the time of termination, less standard
deductions and withholdings. The Company shall thereafter have no further obligations to the Executive under this Agreement. 
 4.2 Termination Without Cause or Resignation for Good Reason. Except as provided in Section 4.3 below, if the Company terminates the Executive’s employment without Cause or if the
Executive resigns for Good Reason (as defined below), the Company shall pay the Executive (i) all Base Salary and accrued but unused vacation benefits and (ii) a pro-rated portion of any bonus amount he has earned, in each case through the
date of termination at the rate in effect at the time of termination, less standard deductions and withholdings. In addition, upon the Executive furnishing to the Company an executed waiver and release of claims (a form of which is attached hereto
as Exhibit A), the Executive shall receive: (i) continuation of his Base Salary then in effect, less standard deductions and withholdings, for a period of six (6) months following the termination date; (ii) in the event
the Executive timely elects continued group health coverage under COBRA, payment by the Company of the premiums associated with such continuation coverage for the Executive and his or her eligible dependents, or coverage under any self-funded plan,
for a period of six (6) months following the termination date, or until Executive is enrolled in the group health insurance plan of another employer, whichever occurs first; and (iii) immediate accelerated vesting of the Option with
respect to that number of shares as if Executive had continued in employment with the Company for a period of six (6) months following the termination date as of Executive’s actual termination date, in accordance with the Option’s
vesting schedule as set forth in the Notice of Grant of Stock Option form or Stock Option Agreement, as applicable. Any applicable group health continuation coverage paid or provided for by the Company shall not include any amounts payable by the
Executive under an Internal Revenue Code Section 125 health care reimbursement plan, which amounts, if any, are the sole responsibility of the Executive. 
  

 4. 

 4.3 Termination Without Cause or Resignation for Good
Reason Following a Change of Control. Notwithstanding Section 4.2 above, if the Company (or its successor) terminates the Executive’s employment without Cause or the Executive resigns for Good Reason within twelve (12) months
following the effective date of a Change of Control of the Company (as defined below), upon the Executive furnishing to the Company an executed waiver and release of claims (a form of which is attached hereto as Exhibit A), the Executive
shall receive: (i) continuation of his Base Salary then in effect, less standard deductions and withholdings, for a period of twelve (12) months following the termination date; (ii) in the event the Executive timely elects continued
group health coverage under COBRA, payment by the Company of the premiums associated with such continuation coverage for the Executive and his or her eligible dependents, or coverage under any self-funded plan, for a period of twelve
(12) months following the termination date, or until Executive is enrolled in the group health insurance plan of another employer, whichever occurs first; and (iii) full accelerated vesting of the Option on the termination date. Any
applicable group health continuation coverage paid or provided for by the Company shall not include any amounts payable by the Executive under an Internal Revenue Code Section 125 health care reimbursement plan, which amounts, if any, are the
sole responsibility of the Executive. 
 4.4 Definitions. For purposes of this
Agreement, the following terms shall have the following meanings: 
 4.4.1 Cause.
“Cause” for the Company to terminate the Executive’s employment hereunder shall mean a reasonable and good faith determination by the Board or any committee thereof that any of the following events has occurred or exists:

 (a) the Executive’s repeated failure satisfactorily to perform the
Executive’s job duties as set forth by the Board; provided that the Executive is provided written notice of such failure and provided a reasonable period to cure such failure by the Company; 
 (b) the Executive’s commission of an act that materially injures the business of the Company;

 (c) the Executive’s commission of any felony or any crime involving fraud,
dishonesty or moral turpitude that is likely to inflict or has inflicted material injury on the business of the Company; or 
 (d) the Executive’s material violation of any provisions of Section 2 or Section 5 hereof and/or the Executive’s Proprietary Information and Inventions Agreement with the
Company. 
  

 5. 

 4.4.2 Change of Control. For purposes of this
Agreement, “Change of Control” shall have the meaning ascribed to it in the Plan, as exists today and may be amended from time to time. 
 4.4.3 Good Reason. For the purposes of this Agreement, the Executive shall be deemed to have resigned for “Good Reason” if he voluntarily resigns immediately
following: 
 (a) a reduction in Executive’s base salary by more than fifteen percent
(15%) (unrelated to an officer-wide reduction in salary); or 
 (b) a relocation of Executive’s
place of employment by more than fifty (50) miles; 
 provided and only if such reduction or relocation is
effected by the Company without the Executive’s written consent. 
 4.5 Survival of
Certain Provisions. Sections 2.2, 2.4, 4, 5, 15, and 17 shall survive the termination of this Agreement. 
  

	 	5.	CONFIDENTIAL AND PROPRIETARY INFORMATION; NONSOLICITATION. 

5.1 As a condition of employment, the Executive agrees to execute and abide by the Proprietary
Information and Inventions Agreement attached hereto as Exhibit B. 
 5.2
While employed by the Company and for one (1) year thereafter, the Executive agrees that in order to protect the Company’s trade secrets and confidential and proprietary information from unauthorized use, the Executive will not, either
directly or through others, solicit or attempt to solicit any employee, consultant or independent contractor of the Company to terminate his or her relationship with the Company in order to become an employee, consultant or independent contractor to
or for any other person or business entity. 
  

	 	6.	 ASSIGNMENT AND BINDING EFFECT. 

 This Agreement shall be binding upon and inure to the benefit of the Executive and the Executive’s heirs, executors,
personal representatives, assigns, administrators and legal representatives. Because of the unique and personal nature of the Executive’s duties under this Agreement, neither this Agreement nor any rights or obligations under this Agreement
shall be assignable by the Executive. This Agreement shall be binding upon and inure to the benefit of the Company and its successors, assigns and legal representatives. 
  

	 	7.	 CHOICE OF LAW. 

 This Agreement is made in San Diego, California. This Agreement shall be construed and interpreted in accordance with the
internal laws of the State of California. 
  

 6. 

	 	8.	 INTEGRATION. 

 This Agreement, including Exhibits A and B, contains the complete, final and exclusive agreement of the Parties relating to the terms and conditions of the Executive’s employment and the termination
of the Executive’s employment, and supersedes any prior or contemporaneous oral or written employment agreements or arrangements between the Parties, including the Consulting Agreement. To the extent this Agreement conflicts with the
Proprietary Information and Inventions Agreement attached as Exhibit B hereto, the Proprietary Information and Inventions Agreement controls. 
  

	 	9.	 AMENDMENT. 

 This Agreement cannot be amended or modified except by a written agreement signed by the Executive and a member of the Board other than the Executive. 
  

	 	10.	 WAIVER. 

 No term, covenant, or condition of this Agreement or any breach thereof shall be deemed waived, except with the written consent of the Party against whom the wavier is claimed, and any waiver or any such
term, covenant, condition or breach shall not be deemed to be a waiver of any preceding or succeeding breach of the same or any other term, covenant, condition or breach. 
  

	 	11.	 SEVERABILITY. 

 The finding by a court of competent jurisdiction of the unenforceability, invalidity or illegality of any provision of this Agreement shall not render any other provision of this Agreement unenforceable,
invalid or illegal. Such court shall have the authority to modify or replace the invalid or unenforceable term or provision with a valid and enforceable term or provision that most accurately represents the Parties’ intentions with respect to
the invalid or unenforceable term or provision. 
  

	 	12.	 INTERPRETATION; CONSTRUCTION. 

 The headings set forth in this Agreement are for convenience of reference only and shall not be used in interpreting this
Agreement. This Agreement has been drafted by legal counsel representing the Company, but the Executive has been encouraged to consult with the Executive’s own independent counsel with respect to the terms of this Agreement. The Parties
acknowledge that each Party and its counsel have reviewed and revised, or have had an opportunity to review and revise, this Agreement, and the normal rule of construction to the effect that any ambiguities are to be resolved against the drafting
party shall not be employed in the interpretation of this Agreement. 
  

	 	13.	 REPRESENTATIONS AND WARRANTIES. 

 The Executive represents and warrants that the Executive is not restricted or prohibited, contractually or otherwise, from
entering into and performing each of the terms and covenants contained in this Agreement, and that Executive’s execution and

  

 7. 

 
performance of this Agreement will not violate or breach any other agreements between the Executive and any other person or entity. The Executive represents and warrants that he is eligible to
work in the U.S., and has provided documentation of such to the Company as required by law. 
  

	 	14.	 COUNTERPARTS. 

 This Agreement may be executed in two counterparts, each of which shall be deemed an original, all of which together shall contribute one and the same instrument. 
  

	 	15.	 ARBITRATION.  

 To ensure the rapid and economical resolution of disputes that may arise in connection with the Executive’s employment with the Company, the Executive and the Company agree that any and all disputes,
claims, or causes of action, in law or equity, arising from or relating to Executive’s employment, or the termination of that employment, will be resolved, to the fullest extent permitted by law, by final, binding and confidential arbitration
in San Diego, California conducted by the Judicial Arbitration and Mediation Services (“JAMS”), or its successors, under the then current rules of JAMS for employment disputes; provided that the arbitrator shall: (a) have the
authority to compel adequate discovery for the resolution of the dispute and to award such relief as would otherwise be permitted by law; and (b) issue a written arbitration decision including the arbitrator’s essential findings and
conclusions and a statement of the award. Both the Executive and the Company shall be entitled to all rights and remedies that either the Executive or the Company would be entitled to pursue in a court of law. The Company shall pay all fees in
excess of those that would be required if the dispute were decided in a court of law, including the arbitrator’s fee. Nothing in this Agreement is intended to prevent either the Executive or the Company from obtaining injunctive relief in court
to prevent irreparable harm pending the conclusion of any such arbitration. Notwithstanding the foregoing, Executive and the Company each have the right to resolve any issue or dispute involving confidential, proprietary or trade secret information,
or intellectual property rights, by court action instead of arbitration. 
  

	 	16.	 TRADE SECRETS OF OTHERS. 

 It is the understanding of both the Company and the Executive that the Executive shall not divulge to the Company and/or its
Affiliates any confidential information or trade secrets belonging to others, including the Executive’s former employers, nor shall the Company and/or its Affiliates seek to elicit from the Executive any such information. Consistent with the
foregoing, the Executive shall not provide to the Company and/or its Affiliates, and the Company and/or its Affiliates shall not request, any documents or copies of documents containing such information. 
  

	 	17.	 ADVERTISING WAIVER. 

 Subject to the Executive’s prior approval, which approval shall not be unreasonably conditioned, delayed or withheld, the Executive agrees to permit the Company and/or its
Affiliates, and persons or other organizations authorized by the Company and/or

  

 8. 

 
its Affiliates, to use, publish and distribute advertising or sales promotional literature concerning the products and/or services of the Company and/or its Affiliates, in which the
Executive’s name and/or pictures of the Executive taken in the course of the Executive’s provision of services to the Company and/or its Affiliates, appear. The Executive hereby waives and releases any claim or right the Executive may
otherwise have arising out of such use, publication or distribution. 
 IN
WITNESS WHEREOF, the Parties have executed this Agreement as of the date first above written. 
  

			
	TRIUS THERAPEUTICS, INC.
		
	 By:
	 	 /s/ David S. Kabakoff

		
	 Dated:
	 	 4/10/07

	
	 EXECUTIVE

	
	 /s/ Jeffrey Stein

	 Jeffrey Stein

		
	 Dated:
	 	 4/5/07

  

 9. 

 EXHIBIT A 
 RELEASE AND WAIVER OF CLAIMS 
 In
consideration of the payments and other benefits set forth in the Employment Agreement dated 2-1-07, to which this form is attached, I, JEFFREY STEIN, hereby furnish TRIUS
THERAPEUTICS, INC. (the “Company”), with the following release and waiver (“Release and Waiver”). 
 In exchange for the consideration provided to me by the Employment Agreement that I am not otherwise entitled to receive, I hereby generally and completely release the Company and
its directors, officers, employees, shareholders, partners, agents, attorneys, predecessors, successors, parent and subsidiary entities, insurers, Affiliates, and assigns from any and all claims, liabilities and obligations, both known and unknown,
that arise out of or are in any way related to events, acts, conduct, or omissions occurring prior to my signing this Release and Waiver. This general release includes, but is not limited to: (1) all claims arising out of or in any way related
to my employment with the Company or the termination of that employment; (2) all claims related to my compensation or benefits from the Company, including, but not limited to, salary, bonuses, commissions, vacation pay, expense reimbursements,
severance pay, fringe benefits, stock, stock options, or any other ownership interests in the Company; (3) all claims for breach of contract, wrongful termination, and breach of the implied covenant of good faith and fair dealing; (4) all
tort claims, including, but not limited to, claims for fraud, defamation, emotional distress, and discharge in violation of public policy; and (5) all federal, state, and local statutory claims, including, but not limited to, claims for
discrimination, harassment, retaliation, attorneys’ fees, or other claims arising under the federal Civil Rights Act of 1964 (as amended), the federal Americans with Disabilities Act of 1990, the federal Age Discrimination in Employment Act of
1967 (as amended) (“ADEA”), and the California Fair Employment and Housing Act (as amended). The foregoing shall not affect in any way my right to receive any severance or other benefits pursuant to and in accordance with the terms
of Section 4 of the Employment Agreement in exchange for this Release and Waiver. 
 I also acknowledge
that I have read and understand Section 1542 of the California Civil Code which reads as follows: “A general release does not extend to claims which the creditor does not know or suspect to exist in his or her favor at the time of
executing the release, which if known by him or her must have materially affected his or her settlement with the debtor.” I hereby expressly waive and relinquish all rights and benefits under that section and any law of any jurisdiction of
similar effect with respect to any claims I may have against the Company. 
 I acknowledge that, among other
rights, I am waiving and releasing any rights I may have under ADEA, that this Release and Waiver is knowing and voluntary, and that the consideration given for this Release and Waiver is in addition to anything of value to which I was already
entitled as an executive of the Company. If I am 40 years of age or older upon execution of this Release and Waiver, I further acknowledge that I have been advised, as required by the Older Workers Benefit Protection Act, that: (a) the release
and waiver granted herein does not relate to claims under the ADEA which may arise after this Release and Waiver is executed; (b) I have the right to consult with an attorney prior to executing this Release and Waiver (although I may choose
voluntarily not to do so);

 
and (c) I have twenty-one (21) days from the date of termination of my employment with the Company in which to consider this Release and Waiver (although I may choose voluntarily to
execute this Release and Waiver earlier); (d) I have seven (7) days following the execution of this Release and Waiver to revoke my consent to this Release and Waiver; and (e) this Release and Waiver shall not be effective until the
seven (7) day revocation period has expired. 
 If I am less than 40 years of age upon execution of this
Release and Waiver, I acknowledge that I have the right to consult with an attorney prior to executing this Release and Waiver (although I may choose voluntarily not to do so); and (c) I have five (5) days from the date of termination of
my employment with the Company in which to consider this Release and Waiver (although I may choose voluntarily to execute this Release and Waiver earlier). 
 I acknowledge my continuing obligations under my Proprietary Information and Inventions Agreement, a copy of which is attached hereto as Exhibit B. Pursuant to the Proprietary
Information and Inventions Agreement I understand that among other things, I must not use or disclose any confidential or proprietary information of the Company and I must immediately return all Company property and documents (including all
embodiments of proprietary information) and all copies thereof in my possession or control. I understand and agree that my right to the severance pay I am receiving in exchange for my agreement to the terms of this Release and Waiver is contingent
upon my continued compliance with my Proprietary Information and Inventions Agreement. 
 This Release and
Waiver constitutes the complete, final and exclusive embodiment of the entire agreement between the Company and me with regard to the subject matter hereof. I am not relying on any promise or representation by the Company that is not expressly
stated herein. This Release and Waiver may only be modified by a writing signed by both me and a duly authorized officer of the Company. 
  

									
	 Date:
	 	  
	 		 	 By:
	 	  

		 		 		 		 	 JEFFREY STEIN

  

 2. 

 EXHIBIT B 
 EMPLOYEE CONFIDENTIALITY AND INVENTIONS ASSIGNMENT AGREEMENT 
  

 1.

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