EX-10.6



 Exhibit 10.6 

AMENDED AND RESTATED EMPLOYMENT AGREEMENT 

THIS AMENDED AND RESTATED EMPLOYMENT AGREEMENT (this “Agreement”) is entered into by and between Crinetics
Pharmaceuticals, Inc., a Delaware corporation (the “Company”), and R. Scott Struthers (“Executive”), and shall be effective as of May 25, 2018 (the “Effective Date”). 

WHEREAS, the Company and Executive previously entered into that certain Employment Agreement, dated October 30, 2015 (the
“Prior Agreement”), which sets forth the terms and conditions of the Executive’s employment with the Company; and 

WHEREAS, the Company desires to amend and restate the Prior Agreement on the terms and conditions set forth in this Agreement. 

NOW, THEREFORE, in consideration of the mutual promises herein contained, the parties agree as follows: 

1.    Definitions. As used in this Agreement, the following terms shall have the following meanings: 

(a)    “Acquisition” means (i) any consolidation or merger of the Company with or into any
other corporation or other entity or person, or any other corporate reorganization, other than any such consolidation, merger or reorganization in which the shares of capital stock of the Company immediately prior to such consolidation, merger or
reorganization, continue to represent a majority of the voting power of the surviving entity (or, if the surviving entity is a wholly owned subsidiary, its parent) immediately after such consolidation, merger or reorganization (provided that, for
the purpose of this Section 1(a), all shares of the Company’s common stock issuable upon exercise of options outstanding immediately prior to such consolidation or merger or upon conversion of Convertible Securities outstanding immediately
prior to such merger or consolidation shall be deemed to be outstanding immediately prior to such merger or consolidation and, if applicable, converted or exchanged in such merger or consolidation on the same terms as the actual outstanding shares
of capital stock are converted or exchanged); or (ii) any transaction or series of related transactions to which the Company is a party in which in excess of fifty percent (50%) of the Company’s voting power is transferred; provided that
an Acquisition shall not include any transaction or series of transactions principally for bona fide equity financing purposes in which cash is received by the Company or any successor or indebtedness of the Company is cancelled or converted or a
combination thereof. 
 (b)    “Asset Transfer” means a sale, lease, exclusive license or other
disposition of all or substantially all of the assets of the Company. 
 (c)    “Board” means
the Board of Directors of the Company. 







 (d)    “Cause” means any of the following: 

(i)     the commission of an act of fraud, embezzlement or dishonesty by Executive, or the commission of some other
illegal act by Executive, that causes material harm to the Company or any successor or affiliate thereof; 
 (ii)
    Executive’s conviction of, or plea of “guilty” or “no contest” to, a felony or any crime involving fraud, dishonesty or moral turpitude under the laws of the United States or any state thereof; 

(iii)     any intentional unauthorized use or disclosure by Executive of confidential information or trade secrets of the
Company or any successor or affiliate thereof; 
 (iv)     Executive’s gross negligence, insubordination or
material violation of any duty of loyalty to the Company or any successor or affiliate thereof, or any other material misconduct on the part of Executive; 

(v)    Executive’s ongoing and repeated failure or refusal to perform or neglect of Executive’s duties as
required by this Agreement, which failure, refusal or neglect continues for fifteen (15) days following Executive’s receipt of written notice from the Board stating with specificity the nature of such failure, refusal or neglect; or 

(vi)     Executive’s intentional, material breach of any Company policy or any contract or agreement between
Executive and the Company or any successor or affiliate thereof; 
 provided, however, that prior to the determination that “Cause”
under clauses (iv), (v) or (vi) of this Section 1(d) has occurred, the Company shall (A) provide to Executive in writing, in reasonable detail, the reasons for the determination that such “Cause” exists, (B) other than
with respect to clause (v) above which specifies the applicable period of time for Executive to remedy his or her breach, afford Executive a reasonable opportunity to remedy any such breach, (C) provide Executive an opportunity to be heard
prior to the final decision to terminate Executive’s employment hereunder for such “Cause” and (D) make any decision that such “Cause” exists in good faith. 

The foregoing definition shall not in any way preclude or restrict the right of the Company or any successor or affiliate thereof to discharge
or dismiss Executive for any other acts or omissions, but such other acts or omissions shall not be deemed, for purposes of this Agreement, to constitute grounds for termination for Cause. 

(e)    “Change in Control” means an Acquisition or Asset Transfer; provided,
however, that, from and after the date on which the Company’s Registration Statement on Form S-1 filed with respect to the Company’s initial public offering becomes effective, “Change in
Control” shall have the meaning given to such term in the Company’s 2018 Incentive Award Plan as in effect on such date. 

Notwithstanding the foregoing, if a Change in Control constitutes a payment event with respect to any payment hereunder that provides for the
deferral of compensation that is subject to Section 409A, to the extent required to avoid the imposition of additional taxes under Section 409A, the transaction or event with respect to such payment shall only constitute a Change in
Control for purposes of the payment timing of such payment if such transaction also constitutes a “change in control event,” as defined in Treasury Regulation Section 1.409A-3(i)(5). 

  
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 (f)    “Code” means the Internal Revenue Code of
1986, as amended from time to time, and the Treasury Regulations and other interpretive guidance issued thereunder. 

(g)    “Convertible Securities” means preferred stock or other stock, options, warrants, purchase
rights or other securities exercisable for or convertible into, additional shares of the Company’s common stock. 

(h)    “Good Reason” means the occurrence of any of the following events or conditions without
Executive’s written consent: 
 (i)    a material diminution in Executive’s authority, duties or
responsibilities; 
 (ii)    a material diminution in Executive’s base compensation, unless such a reduction is
imposed across-the-board to senior management of the Company; 

(iii)    a material change in the geographic location at which Executive must perform his or her duties; or 

(iv)    any other action or inaction that constitutes a material breach by the Company or any successor or affiliate of
its obligations to Executive under this Agreement. 
 Executive must provide written notice to the Company of the occurrence of any of the
foregoing events or conditions without Executive’s written consent within sixty (60) days of the occurrence of such event. The Company or any successor or affiliate shall have a period of thirty (30) days to cure such event or
condition after receipt of written notice of such event from Executive. Executive’s Separation from Service by reason of resignation from employment with the Company for Good Reason must occur within thirty (30) days following the
expiration of the foregoing thirty (30) day cure period. 
 (i)    “Involuntary
Termination” means (i) Executive’s Separation from Service by reason of Executive’s discharge by the Company other than for Cause, or (ii) Executive’s Separation from Service by reason of Executive’s
resignation of employment with the Company for Good Reason. Executive’s Separation from Service by reason of Executive’s death or discharge by the Company following Executive’s Permanent Disability shall not constitute an Involuntary
Termination. 
 (j)    Executive’s “Permanent Disability” shall be deemed to have occurred
if Executive shall become physically or mentally incapacitated or disabled or otherwise unable fully to discharge his or her duties hereunder for a period of ninety (90) consecutive calendar days or for one hundred twenty (120) calendar
days in any one hundred eighty (180) calendar-day period. The existence of Executive’s Permanent Disability shall be determined by the Company on the advice of a physician chosen by the Company and
the Company reserves the right to have Executive examined by a physician chosen by the Company at the Company’s expense. 

(k)    “Separation from Service,” with respect to Executive, means Executive’s
“separation from service,” as defined in Treasury Regulation Section 1.409A-1(h). 

  
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 (l)    “Stock Awards” means all stock options,
restricted stock and such other awards granted pursuant to the Company’s stock option and equity incentive award plans or agreements and any shares of stock issued upon exercise thereof; provided that “Stock Awards” shall not
include those shares of the Company’s common stock owned by Executive as of the date hereof and issued to Executive pursuant to that certain Restricted Stock Purchase Agreement dated as of July 31, 2011 (the “Founders’
Shares”), which Founders’ Shares are subject to the terms of the Stock Restriction Agreement of even date herewith between Executive and the Company (the “Stock Restriction Agreement”). 

2.     Services to Be Rendered. 

(a)    Duties and Responsibilities. Executive shall serve as President, Chief Executive Officer, Secretary and
Treasurer of the Company. In the performance of such duties, Executive shall report directly to the Board and shall be subject to the direction of the Board and to such limits upon Executive’s authority as the Board may from time to time
impose. Executive hereby consents to serve as an officer and/or director of the Company or any subsidiary or affiliate thereof without any additional salary or compensation, if so requested by the Board. Executive shall be employed by the Company on
a full time basis. Executive’s primary place of work shall be the Company’s offices in San Diego, California, or, with the Company’s consent, at any other place at which the Company maintains an office; provided,
however, that the Company may from time to time require Executive to travel temporarily to other locations in connection with the Company’s business. Executive shall be subject to and comply with the policies and procedures generally
applicable to senior executives of the Company to the extent the same are not inconsistent with any term of this Agreement. 

(b)    Exclusive Services. Executive shall at all times faithfully, industriously and to the best of his or her
ability, experience and talent perform to the satisfaction of the Board all of the duties that may be assigned to Executive hereunder and shall devote substantially all of his or her productive time and efforts to the performance of such
duties. Subject to the terms of the Proprietary Information and Inventions Agreement referred to in Section 5(b), this shall not preclude Executive from (i) serving on industry trade, civic, or charitable boards or committees;
(ii) delivering lectures or fulfilling speaking engagements; (iii) serving on the board of directors or other similar governance body of any entity, subject to the consent of the Board, such consent not to be unreasonably withheld; or
(iv) managing personal, family and other investments, provided such activities do not interfere with his or her duties to the Company, as determined in good faith by the Board. Executive agrees that he or she will not join any boards, other
than community and civic boards (which do not interfere with his or her duties to the Company), without the prior approval of the Board.  

3.    Compensation and Benefits. The Company shall pay or provide, as the case may be, to Executive the
compensation and other benefits and rights set forth in this Section 3. 
 (a)    Base Salary. The Company
shall pay to Executive a base salary of $350,000 per year, payable in accordance with the Company’s usual pay practices (and in any event no less frequently than monthly); provided, however, that, effective on the date on which
the Company’s Registration Statement on Form S-1 filed with respect to the Company’s initial public offering becomes effective, Executive’s base salary shall be increased to $495,000.
Executive’s base salary shall be subject to review annually by and at the sole discretion of the Compensation Committee of the Board or its designee. 

  
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 (b)    Bonus. Executive shall participate in any bonus plan that the
Board or its designee may approve for the senior executives of the Company. Executive’s target bonus under the Company’s annual bonus plan shall be fifty percent (50%) of Executive’s base salary. 

(c)    Benefits. Executive shall be entitled to participate in benefits under the Company’s benefit plans and
arrangements, including, without limitation, any employee benefit plan or arrangement made available in the future by the Company to its senior executives, subject to and on a basis consistent with the terms, conditions and overall administration of
such plans and arrangements. The Company shall have the right to amend or delete any such benefit plan or arrangement made available by the Company to its senior executives and not otherwise specifically provided for herein. 

(d)    Expenses. The Company shall reimburse Executive for reasonable out-of-pocket business expenses incurred in connection with the performance of his or her duties hereunder, subject to such policies as the Company may from time to time establish, and Executive furnishing
the Company with evidence in the form of receipts satisfactory to the Company substantiating the claimed expenditures. 

(e)    Paid Time Off. Executive shall be entitled to such periods of paid time off (“PTO”)
each year as provided from time to time under the Company’s PTO policy and as otherwise provided for senior executive officers. 

(f)    Equity Plans. Executive shall be entitled to participate in any equity or other employee benefit plan that
is generally available to executives of the Company. Except as otherwise provided in this Agreement, Executive’s participation in and benefits under any such plan shall be on the terms and subject to the conditions specified in the governing
document of the particular plan. 
 (g)    Stock Award Acceleration. 

(i)    Subject to Section 4(d), in the event of Executive’s Separation from Service by reason of
Executive’s death or discharge by the Company following Executive’s Permanent Disability, the vesting and/or exercisability of 100% of Executive’s outstanding unvested Stock Awards shall be automatically accelerated on the date of
Executive’s Separation from Service. 
 (ii)    Subject to Section 4(d), in the event of a Change in Control,
the vesting and/or exercisability of 100% of Executive’s outstanding unvested Stock Awards shall be automatically accelerated on the first to occur of (A) Executive’s Involuntary Termination following such Change in Control, or
(B) the first anniversary of the closing of such Change in Control. 
 (iii)    Subject to
Section 4(d), in the event of Executive’s Involuntary Termination prior to the occurrence of a Change in Control, the vesting and/or exercisability of any outstanding unvested portion of each of Executive’s Stock Awards shall be
automatically accelerated as to the number of Stock Awards that would vest over the twelve (12) month period following the date of Executive’s Separation from Service had Executive remained continuously employed by the Company during such
period. 

  
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 (iv)    The vesting pursuant to clauses (i), (ii) and (iii) of this
Section 3(g) shall be cumulative. The foregoing provisions are hereby deemed to be a part of each Stock Award and to supersede any less favorable provision in any agreement or plan regarding such Stock Award. 

4.    Severance. Executive shall be entitled to receive benefits upon a Separation from Service only as set forth
in this Section 4: 
 (a)    At-Will Employment; Termination. The
Company and Executive acknowledge that Executive’s employment is and shall continue to be at-will, as defined under applicable law, and that Executive’s employment with the Company may be terminated
by either party at any time for any or no reason, with or without notice. If Executive’s employment terminates for any reason, Executive shall not be entitled to any payments, benefits, damages, awards or compensation other than as provided in
this Agreement. Executive’s employment under this Agreement shall be terminated immediately on the death of Executive. 

(b)    Severance Upon Involuntary Termination.    Subject to Sections 4(d) and 9(o) and
Executive’s continued compliance with Section 5, if Executive’s employment is Involuntarily Terminated, Executive shall be entitled to receive, in lieu of any severance benefits to which Executive may otherwise be entitled under any
severance plan or program of the Company, the benefits provided below: 
 (i)    the Company shall pay to Executive his
or her fully earned but unpaid base salary, when due, through the date of Executive’s Involuntary Termination at the rate then in effect, accrued and unused PTO, plus all other benefits, if any, under any Company group retirement plan,
nonqualified deferred compensation plan, equity award plan or agreement (other than any such plan or agreement pertaining to Stock Awards whose treatment is prescribed by Section 3(g) above), health benefits plan or other Company group benefit
plan to which Executive may be entitled pursuant to the terms of such plans or agreements at the time of Executive’s Involuntary Termination (the “Accrued Obligations”); 

(ii)    Executive shall be entitled to receive severance pay in an amount equal to twelve (12) multiplied by
Executive’s monthly base salary as in effect immediately prior to the date of Executive’s Involuntary Termination, which amount shall be payable in a lump sum sixty (60) days following Executive’s Involuntary Termination; and

 (iii)     for the period beginning on the date of Executive’s Separation from Service and ending on the date
which is twelve (12) full months following the date of Executive’s Separation from Service (or, if earlier, (1) the date on which the applicable continuation period under the Consolidated Omnibus Budget Reconciliation Act of 1985, as
amended (“COBRA”) expires or (2) the date Executive becomes eligible to receive the equivalent or increased healthcare coverage by means of subsequent employment or self-employment) (such period, the “COBRA
Coverage Period”), if Executive and/or his or her eligible dependents who were covered under the Company’s health insurance plans as of the date of Executive’s Separation from Service elect to have COBRA coverage and are
eligible for such coverage, the Company shall pay for or reimburse Executive on a monthly basis for an amount equal to (A) the monthly premium Executive and/or his or her covered dependents, as applicable, are required to pay for continuation
coverage pursuant to COBRA for Executive and/or his or her eligible dependents, as applicable, who were covered under the 

  
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Company’s health plans as of the date of Executive’s Separation from Service (calculated by reference to the premium as of the date of Executive’s Separation from Service) less
(B) the amount Executive would have had to pay to receive group health coverage for Executive and/or his or her covered dependents, as applicable, based on the cost sharing levels in effect on the date of Executive’s Separation from
Service. If any of the Company’s health benefits are self-funded as of the date of Executive’s Separation from Service, or if the Company cannot provide the foregoing benefits in a manner that is exempt from Section 409A (as defined
below) or that is otherwise compliant with applicable law (including, without limitation, Section 2716 of the Public Health Service Act), instead of providing the payments or reimbursements as set forth above, the Company shall instead pay to
Executive the foregoing monthly amount as a taxable monthly payment for the COBRA Coverage Period (or any remaining portion thereof). Executive shall be solely responsible for all matters relating to continuation of coverage pursuant to COBRA,
including, without limitation, the election of such coverage and the timely payment of premiums. Executive shall notify the Company immediately if Executive becomes eligible to receive the equivalent or increased healthcare coverage by means of
subsequent employment or self-employment. 
 (iv)    Notwithstanding anything to the contrary in this Section 4(b),
and subject to Sections 4(d) and 9(o) and Executive’s continued compliance with Section 5, in the event of Executive’s Involuntary Termination within twelve (12) months following a Change in Control, (A) the references to
twelve (12) months in clauses (ii) and (iii) above shall be increased to eighteen (18) months, and (B) Executive shall be entitled to receive, in addition to the severance benefits described in clauses (i), (ii) and
(iii) above, an amount equal to Executive’s target bonus for the year in which Executive’s Involuntary Termination occurs, which amount shall be payable in a lump sum sixty (60) days following Executive’s Involuntary
Termination. 
 (c)    Termination for Cause, Voluntary Resignation Without Good Reason, Death or Termination for
Permanent Disability. In the event of Executive’s termination of employment as a result of Executive’s discharge by the Company for Cause, Executive’s resignation without Good Reason, Executive’s death or Executive’s
termination of employment following Executive’s Permanent Disability, the Company shall not have any other or further obligations to Executive under this Agreement (including any financial obligations) except that Executive shall be entitled to
receive the Accrued Obligations. The foregoing shall be in addition to, and not in lieu of, any and all other rights and remedies which may be available to the Company under the circumstances, whether at law or in equity. 

(d)    Release. As a condition to Executive’s receipt of any post-termination benefits pursuant to
Section 4(b) above, Executive (or, in the event of Executive’s incapacity as a result of his or her Permanent Disability, Executive’s legal representative) shall execute and not revoke a general release of all claims in favor of the
Company (the “Release”) in the form attached hereto as Exhibit A. In the event the Release does not become effective within the fifty-five (55) day period following the date of Executive’s Separation from Service,
Executive shall not be entitled to the aforesaid payments and benefits. 
 (e)    Exclusive Remedy. Except as
otherwise expressly required by law (e.g., COBRA) or as specifically provided herein, all of Executive’s rights to salary, severance, benefits, bonuses and other amounts hereunder (if any) accruing after the termination of Executive’s
employment shall cease upon such termination. In the event of Executive’s termination of 

  
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employment with the Company, Executive’s sole remedy shall be to receive the payments and benefits described in Section 3(g) and this Section 4. In addition, Executive acknowledges
and agrees that he or she is not entitled to any reimbursement by the Company for any taxes payable by Executive as a result of the payments and benefits received by Executive pursuant to Section 3(g) and this Section 4, including, without
limitation, any excise tax imposed by Section 4999 of the Code. Any payments made to Executive under this Section 4 shall be inclusive of any amounts or benefits to which Executive may be entitled pursuant to the Worker Adjustment and
Retraining Notification Act, 29 U.S.C. Sections 2101 et seq., and the Department of Labor regulations thereunder, or any similar state statute. 

(f)    No Mitigation. Except as otherwise provided in Section 4(b)(iii) above, Executive shall not be required
to mitigate the amount of any payment provided for in this Section 4 by seeking other employment or otherwise, nor shall the amount of any payment or benefit provided for in this Section 4 be reduced by any compensation earned by Executive
as the result of employment by another employer or self-employment or by retirement benefits; provided, however, that loans, advances or other amounts owed by Executive to the Company may be offset by the Company against amounts
payable to Executive under this Section 4. 
 (g)    Return of the Company’s Property. In the event of
Executive’s termination of employment for any reason, the Company shall have the right, at its option, to require Executive to vacate his or her offices prior to or on the effective date of separation and to cease all activities on the
Company’s behalf. Upon Executive’s termination of employment in any manner, as a condition to Executive’s receipt of any severance benefits described in this Agreement, Executive shall immediately surrender to the Company all lists,
books and records of, or in connection with, the Company’s business, and all other property belonging to the Company, it being distinctly understood that all such lists, books and records, and other documents, are the property of the Company.
Executive shall deliver to the Company a signed statement certifying compliance with this Section 4(g) prior to the receipt of any severance benefits described in this Agreement. 

(h)    Deemed Resignation. Upon termination of Executive’s employment for any reason, Executive shall be
deemed to have resigned from all offices and directorships, if any, then held with the Company or any of its affiliates, and, at the Company’s request, Executive shall execute such documents as are necessary or desirable to effectuate such
resignations. 
 5.    Certain Covenants. 

(a)    Noncompetition. Except as may otherwise be approved by the Board, during the term of Executive’s
employment, Executive shall not have any ownership interest (of record or beneficial) in, or have any interest as an employee, salesman, consultant, officer or director in, or otherwise aid or assist in any manner, any firm, corporation,
partnership, proprietorship or other business that engages in any county, city or part thereof in the United States and/or any foreign country in a business which competes directly or indirectly (as determined by the Board) with the Company’s
business in such county, city or part thereof, so long as the Company, or any successor in interest of the Company to the business and goodwill of the Company, remains engaged in such business in such county, city or part thereof or continues to
solicit customers or potential customers therein; provided, however, that Executive may own, directly or indirectly, solely as an investment, securities of any entity which are traded on any national securities exchange if Executive
(i) is not 

  
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a controlling person of, or a member of a group which controls, such entity; or (ii) does not, directly or indirectly, own one percent (1%) or more of any class of securities of any such
entity; provided, further, that Executive’s continued ownership interest in ScienceMedia shall not be considered a violation of this Agreement. 

(b)    Confidential Information. Executive and the Company have entered into the Company’s standard employee
proprietary information and inventions agreement (the “Employee Proprietary Information and Inventions Agreement”). Executive agrees to perform each and every obligation of Executive therein contained. 

(c)    Solicitation of Employees. Executive shall not during the term of Executive’s employment and for a
period of twelve (12) months following Executive’s Separation from Service (the “Restricted Period”), directly or indirectly, solicit or encourage to leave the employment of the Company or any of its affiliates, any
employee of the Company or any of its affiliates. 
 (d)    Solicitation of Consultants. Executive shall not
during the term of Executive’s employment and for the Restricted Period, directly or indirectly, hire, solicit or encourage to cease work with the Company or any of its affiliates any consultant then under contract with the Company or any of
its affiliates within one year of the termination of such consultant’s engagement by the Company or any of its affiliates. 

(e)    Rights and Remedies Upon Breach. If Executive breaches or threatens to commit a breach of any of the
provisions of this Section 5 (the “Restrictive Covenants”), the Company shall have the following rights and remedies, each of which rights and remedies shall be independent of the other and severally enforceable, and all of
which rights and remedies shall be in addition to, and not in lieu of, any other rights and remedies available to the Company under law or in equity: 

(i)    Specific Performance. The right and remedy to have the Restrictive Covenants specifically enforced by any
court having equity jurisdiction, all without the need to post a bond or any other security or to prove any amount of actual damage or that money damages would not provide an adequate remedy, it being acknowledged and agreed that any such breach or
threatened breach will cause irreparable injury to the Company and that money damages will not provide adequate remedy to the Company; and 

(ii)    Accounting and Indemnification. The right and remedy to require Executive (A) to account for and pay
over to the Company all compensation, profits, monies, accruals, increments or other benefits derived or received by Executive or any associated party deriving such benefits as a result of any such breach of the Restrictive Covenants; and
(B) to indemnify the Company against any other losses, damages (including special and consequential damages), costs and expenses, including actual attorneys’ fees and court costs, which may be incurred by them and which result from or
arise out of any such breach or threatened breach of the Restrictive Covenants. 
 (f)    Severability of
Covenants/Blue Pencilling. If any court determines that any of the Restrictive Covenants, or any part thereof, is invalid or unenforceable, the remainder of the Restrictive Covenants shall not thereby be affected and shall be given full effect,
without regard to 

  
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the invalid portions. If any court determines that any of the Restrictive Covenants, or any part thereof, are unenforceable because of the duration of such provision or the area covered thereby,
such court shall have the power to reduce the duration or area of such provision and, in its reduced form, such provision shall then be enforceable and shall be enforced. Executive hereby waives any and all right to attack the validity of the
Restrictive Covenants on the grounds of the breadth of their geographic scope or the length of their term. 

(g)    Enforceability in Jurisdictions. The Company and Executive intend to and do hereby confer jurisdiction to
enforce the Restrictive Covenants upon the courts of any jurisdiction within the geographical scope of such covenants. If the courts of any one or more of such jurisdictions hold the Restrictive Covenants wholly unenforceable by reason of the
breadth of such scope or otherwise, it is the intention of the Company and Executive that such determination not bar or in any way affect the right of the Company to the relief provided above in the courts of any other jurisdiction within the
geographical scope of such covenants, as to breaches of such covenants in such other respective jurisdictions, such covenants as they relate to each jurisdiction being, for this purpose, severable into diverse and independent covenants. 

(h)    Whistleblower Provision. Nothing herein shall be construed to prohibit Executive from communicating directly
with, cooperating with, or providing information to, any government regulator, including, but not limited to, the U.S. Securities and Exchange Commission, the U.S. Commodity Futures Trading Commission, or the U.S. Department of Justice. Executive
acknowledges that the Company has provided Executive with the following notice of immunity rights in compliance with the requirements of the Defend Trade Secrets Act: (i) Executive shall not be held criminally or civilly liable under any
Federal or State trade secret law for the disclosure of proprietary information of the Company that is made in confidence to a Federal, State, or local government official or to an attorney solely for the purpose of reporting or investigating a
suspected violation of law, (ii) Executive shall not be held criminally or civilly liable under any Federal or State trade secret law for the disclosure of proprietary information of the Company that is made in a complaint or other document
filed in a lawsuit or other proceeding, if such filing is made under seal and (iii) if Executive files a lawsuit for retaliation by the Company for reporting a suspected violation of law, Executive may disclose the proprietary information to my
attorney and use the proprietary information in the court proceeding, if Executive files any document containing the proprietary information under seal, and does not disclose the proprietary information, except pursuant to court order. 

(i)    Definitions. For purposes of this Section 5, the term “Company” means not only
Crinetics Pharmaceuticals, Inc., but also any company, partnership or entity which, directly or indirectly, controls, is controlled by or is under common control with Crinetics Pharmaceuticals, Inc. 

6.    Insurance; Indemnification. 

(a)    Insurance. The Company shall have the right to take out life, health, accident, “key-man” or other insurance covering Executive, in the name of the Company and at the Company’s expense in any amount deemed appropriate by the Company. Executive shall assist the Company in
obtaining such insurance, including, without limitation, submitting to any required examinations and providing information and data required by insurance companies. 

  
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 (b)    Indemnification. Executive will be provided with
indemnification against third party claims related to his or her work for the Company as required by Delaware law. The Company shall provide Executive with directors and officers liability insurance coverage at least as favorable as that which the
Company may maintain from time to time for members of the Board and other executive officers. 

7.    Arbitration. Any dispute, claim or controversy based on, arising out of or relating to Executive’s
employment or this Agreement shall be settled by final and binding arbitration in San Diego, California, before a single neutral arbitrator in accordance with the National Rules for the Resolution of Employment Disputes (the
“Rules”) of the American Arbitration Association, and judgment on the award rendered by the arbitrator may be entered in any court having jurisdiction. The Rules may be found online at www.adr.org. Arbitration may be
compelled pursuant to the California Arbitration Act (Code of Civil Procedure §§ 1280 et seq.). If the parties are unable to agree upon an arbitrator, one shall be appointed by the AAA in accordance with its Rules. Each party
shall pay the fees of its own attorneys, the expenses of its witnesses and all other expenses connected with presenting its case; however, Executive and the Company agree that, to the extent permitted by law, the arbitrator may, in his or her
discretion, award reasonable attorneys’ fees to the prevailing party. Other costs of the arbitration, including the cost of any record or transcripts of the arbitration, AAA’s administrative fees, the fee of the arbitrator, and all other
fees and costs, shall be borne by the Company. This Section 7 is intended to be the exclusive method for resolving any and all claims by the parties against each other for payment of damages under this Agreement or relating to Executive’s
employment; provided, however, that Executive shall retain the right to file administrative charges with or seek relief through any government agency of competent jurisdiction, and to participate in any government investigation,
including but not limited to (i) claims for workers’ compensation, state disability insurance or unemployment insurance; (ii) claims for unpaid wages or waiting time penalties brought before the California Division of Labor Standards
Enforcement; provided, however, that any appeal from an award or from denial of an award of wages and/or waiting time penalties shall be arbitrated pursuant to the terms of this Agreement; and (iii) claims for administrative
relief from the United States Equal Employment Opportunity Commission and/or the California Department of Fair Employment and Housing (or any similar agency in any applicable jurisdiction other than California); provided, further, that
Executive shall not be entitled to obtain any monetary relief through such agencies other than workers’ compensation benefits or unemployment insurance benefits. This Agreement shall not limit either party’s right to obtain any provisional
remedy, including, without limitation, injunctive or similar relief, from any court of competent jurisdiction as may be necessary to protect their rights and interests pending the outcome of arbitration, including without limitation injunctive
relief, in any court of competent jurisdiction pursuant to California Code of Civil Procedure § 1281.8 or any similar statute of an applicable jurisdiction. Seeking any such relief shall not be deemed to be a waiver of such party’s right
to compel arbitration. Both Executive and the Company expressly waive their right to a jury trial. 
 8.    General
Relationship. Executive shall be considered an employee of the Company within the meaning of all federal, state and local laws and regulations including, but not limited to, laws and regulations governing unemployment insurance, workers’
compensation, industrial accident, labor and taxes. 

  
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 9.    Miscellaneous. 

(a)    Modification; Prior Claims. This Agreement, the Stock Restriction Agreement and the Employee Proprietary
Information and Inventions Agreement (and the other documents referenced therein) set forth the entire understanding of the parties with respect to the subject matter hereof, and supersede all existing agreements between them concerning such subject
matter, including, without limitation, the Prior Agreement. This Agreement may be amended or modified only with the written consent of Executive and an authorized representative of the Company. No oral waiver, amendment or modification will be
effective under any circumstances whatsoever. 
 (b)    Assignment; Assumption by Successor. The rights of the
Company under this Agreement may, without the consent of Executive, be assigned by the Company, in its sole and unfettered discretion, to any person, firm, corporation or other business entity which at any time, whether by purchase, merger or
otherwise, directly or indirectly, acquires all or substantially all of the assets or business of the Company. The Company will require any successor (whether direct or indirect, by purchase, merger or otherwise) to all or substantially all of the
business or assets of the Company expressly to assume and to agree to perform this Agreement in the same manner and to the same extent that the Company would be required to perform it if no such succession had taken place; provided,
however, that no such assumption shall relieve the Company of its obligations hereunder. As used in this Agreement, the “Company” shall mean the Company as hereinbefore defined and any successor to its business and/or
assets as aforesaid which assumes and agrees to perform this Agreement by operation of law or otherwise. 

(c)    Survival. The covenants, agreements, representations and warranties contained in or made in
Sections 3(g), 4, 5, 6, 7 and 9 of this Agreement shall survive any Executive’s termination of employment. 

(d)    Third-Party Beneficiaries. This Agreement does not create,
and shall not be construed as creating, any rights enforceable by any person not a party to this Agreement. 

(e)    Waiver. The failure of either party hereto at any time to enforce performance by the other party of any
provision of this Agreement shall in no way affect such party’s rights thereafter to enforce the same, nor shall the waiver by either party of any breach of any provision hereof be deemed to be a waiver by such party of any other breach of the
same or any other provision hereof. 
 (f)    Section Headings. The headings of the several sections in this
Agreement are inserted solely for the convenience of the parties and are not a part of and are not intended to govern, limit or aid in the construction of any term or provision hereof. 

(g)    Notices. Any notice required or permitted by this Agreement shall be in writing and shall be delivered as
follows with notice deemed given as indicated: (i) by personal delivery when delivered personally; (ii) by overnight courier upon written verification of receipt; (iii) by email, telecopy or facsimile transmission upon acknowledgment
of receipt of electronic transmission; or (iv) by certified or registered mail, return receipt requested, upon verification of receipt. Notice shall be sent to Executive at the address listed on the Company’s personnel records and to the
Company at its principal place of business, or such other address as either party may specify in writing. 

  
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 (h)    Severability. All Sections, clauses and covenants contained in
this Agreement are severable, and in the event any of them shall be held to be invalid by any court, this Agreement shall be interpreted as if such invalid Sections, clauses or covenants were not contained herein. 

(i)    Governing Law and Venue. This Agreement is to be governed by and construed in accordance with the laws of
the State of California applicable to contracts made and to be performed wholly within such State, and without regard to the conflicts of laws principles thereof. Except as provided in Sections 5 and 7, any suit brought hereon shall be brought
in the state or federal courts sitting in San Diego, California, the parties hereto hereby waiving any claim or defense that such forum is not convenient or proper. Each party hereby agrees that any such court shall have in personam jurisdiction
over it and consents to service of process in any manner authorized by California law. 
 (j)    Non-transferability of Interest. None of the rights of Executive to receive any form of compensation payable pursuant to this Agreement shall be assignable or transferable except through a testamentary
disposition or by the laws of descent and distribution upon the death of Executive. Any attempted assignment, transfer, conveyance, or other disposition (other than as aforesaid) of any interest in the rights of Executive to receive any form of
compensation to be made by the Company pursuant to this Agreement shall be void. 
 (k)    Gender. Where the
context so requires, the use of the masculine gender shall include the feminine and/or neuter genders and the singular shall include the plural, and vice versa, and the word “person” shall include any corporation, firm, partnership or
other form of association. 
 (l)    Counterparts; Facsimile or .pdf Signatures. This Agreement may be executed
in any number of counterparts, each of which when so executed and delivered will be deemed an original, and all of which together shall constitute one and the same agreement. This Agreement may be executed and delivered by facsimile or by .pdf file
and upon such delivery the facsimile or .pdf signature will be deemed to have the same effect as if the original signature had been delivered to the other party. 

(m)    Construction. The language in all parts of this Agreement shall in all cases be construed simply, according
to its fair meaning, and not strictly for or against any of the parties hereto. Without limitation, there shall be no presumption against any party on the ground that such party was responsible for drafting this Agreement or any part thereof. 

(n)    Withholding and other Deductions. All compensation payable to Executive hereunder shall be subject to such
deductions as the Company is from time to time required to make pursuant to law, governmental regulation or order. 
 (o)
    Code Section 409A. 
 (i) This Agreement is not intended to provide for any deferral of compensation
subject to Section 409A of the Code, and, accordingly, the severance payments payable under Sections 4(b)(ii) and 4(b)(iv) shall be paid no later than the later of: (A) the fifteenth (15th) day of the third month following Executive’s
first taxable year in which such amounts are no longer subject to a substantial risk of forfeiture, and (B) the fifteenth (15th) day of the third month 

  
 13 








 
following first taxable year of the Company in which such amounts are is no longer subject to substantial risk of forfeiture, as determined in accordance with Code Section 409A and any
Treasury Regulations and other guidance issued thereunder. To the extent applicable, this Agreement shall be interpreted in accordance with Code Section 409A and Department of Treasury regulations and other interpretive guidance issued
thereunder. Each series of installment payments made under this Agreement is hereby designated as a series of “separate payments” within the meaning of Section 409A of the Code.    For purposes of this Agreement,
all references to Executive’s “termination of employment” shall mean Executive’s Separation from Service. 

(ii)    If Executive is a “specified employee” (as defined in Section 409A of the Code), as determined by
the Company in accordance with Section 409A of the Code, on the date of Executive’s Separation from Service, to the extent that the payments or benefits under this Agreement are subject to Section 409A of the Code and the delayed
payment or distribution of all or any portion of such amounts to which Executive is entitled under this Agreement is required in order to avoid a prohibited distribution under Section 409A(a)(2)(B)(i) of the Code, then such portion deferred
pursuant to this Section 9(o)(ii) shall be paid or distributed to Executive in a lump sum on the earlier of (A) the date that is six (6)-months following Executive’s Separation from Service, (B) the date of Executive’s death
or (C) the earliest date as is permitted under Section 409A of the Code. Any remaining payments due under the Agreement shall be paid as otherwise provided herein. 

(iii)    To the extent applicable, this Agreement shall be interpreted in accordance with the applicable exemptions from
Section 409A of the Code. If Executive and the Company determine that any payments or benefits payable under this Agreement intended to comply with Sections 409A(a)(2), (3) and (4) of the Code do not comply with Section 409A of the
Code, Executive and the Company agree to amend this Agreement, or take such other actions as Executive and the Company deem reasonably necessary or appropriate, to comply with the requirements of Section 409A of the Code and the Treasury Regulations
thereunder (and any applicable transition relief) while preserving the economic agreement of the parties. To the extent that any provision in this Agreement is ambiguous as to its compliance with Section 409A of the Code, the provision
shall be read in such a manner that no payments payable under this Agreement shall be subject to an “additional tax” as defined in Section 409A(a)(1)(B) of the Code. 

(iv)    Any reimbursement of expenses or in-kind benefits payable under this
Agreement shall be made in accordance with Treasury Regulation Section 1.409A-3(i)(1)(iv) and shall be paid on or before the last day of Executive’s taxable year following the taxable year in which
Executive incurred the expenses. The amount of expenses reimbursed or in-kind benefits payable during any taxable year of Executive’s shall not affect the amount eligible for reimbursement or in-kind benefits payable in any other taxable year of Executive’s, and Executive’s right to reimbursement for such amounts shall not be subject to liquidation or exchange for any other benefit. 

[SIGNATURE PAGE FOLLOWS] 

  
 14 








 IN WITNESS WHEREOF, the parties have executed this Agreement as of the date first set forth
above. 
  

			
	 CRINETICS PHARMACEUTICALS,
INC.

		
	 By:
	 	 /s/ Marc Wilson

	 Name:
	 	Marc Wilson
	 Title:
	 	Chief Financial Officer & Secretary
	
	 EXECUTIVE

	
	 /s/ R. Scott Struthers

	 R. Scott Struthers




  
 SIGNATURE PAGE TO AMENDED
AND RESTATED EMPLOYMENT AGREEMENT 








 EXHIBIT A 

GENERAL RELEASE OF CLAIMS 

[The language in this Release may change based on legal developments and evolving best practices; this form is provided as an example of
what will be included in the final Release document.] 
 This General Release of Claims (“Release”) is entered
into as of this             day of             ,         , between R. Scott Struthers
(“Executive”), and Crinetics Pharmaceuticals, Inc. (the “Company”) (collectively referred to herein as the “Parties”). 

WHEREAS, Executive and the Company are parties to that certain Amended and Restated Employment Agreement dated as of May 25, 2018 (the
“Agreement”); 
 WHEREAS, the Parties agree that Executive is entitled to certain severance benefits under the
Agreement, subject to Executive’s execution of this Release; and 
 WHEREAS, the Company and Executive now wish to fully and finally to
resolve all matters between them. 
 NOW, THEREFORE, in consideration of, and subject to, the severance benefits payable to Executive
pursuant to the Agreement, the adequacy of which is hereby acknowledged by Executive, and which Executive acknowledges that he or she would not otherwise be entitled to receive, Executive and the Company hereby agree as follows: 

1.    General Release of Claims by Executive. 

(a)    Executive, on behalf of himself or herself and his or her executors, heirs, administrators, representatives and
assigns, hereby agrees to release and forever discharge the Company and all predecessors, successors and their respective parent corporations, affiliates, related, and/or subsidiary entities, and all of their past and present investors, directors,
shareholders, officers, general or limited partners, employees, attorneys, agents and representatives, and the employee benefit plans in which Executive is or has been a participant by virtue of his or her employment with or service to the Company
(collectively, the “Company Releasees”), from any and all claims, debts, demands, accounts, judgments, rights, causes of action, equitable relief, damages, costs, charges, complaints, obligations, promises, agreements,
controversies, suits, expenses, compensation, responsibility and liability of every kind and character whatsoever (including attorneys’ fees and costs), whether in law or equity, known or unknown, asserted or unasserted, suspected or
unsuspected (collectively, “Claims”), which Executive has or may have had against such Company Releasees based on any events or circumstances arising or occurring on or prior to the date hereof or on or prior to the date
hereof, arising directly or indirectly out of, relating to, or in any other way involving in any manner whatsoever Executive’s employment by or service to the Company or the termination thereof, including any and all claims arising under
federal, state, or local laws relating to employment, including without limitation claims of wrongful discharge, breach of express or implied contract, fraud, misrepresentation, defamation, or liability in tort, and claims


  
 1 








 
of any kind that may be brought in any court or administrative agency including, without limitation, claims under Title VII of the Civil Rights Act of 1964, as amended, 42 U.S.C.
Section 2000, et seq.; the Americans with Disabilities Act, as amended, 42 U.S.C. § 12101 et seq.; the Rehabilitation Act of 1973, as amended, 29 U.S.C. § 701 et seq.; the
Civil Rights Act of 1866, and the Civil Rights Act of 1991; 42 U.S.C. Section 1981, et seq.; the Age Discrimination in Employment Act, as amended, 29 U.S.C. Section 621, et seq. (the
“ADEA”); the Equal Pay Act, as amended, 29 U.S.C. Section 206(d); regulations of the Office of Federal Contract Compliance, 41 C.F.R. Section 60, et seq.; the Family and Medical Leave Act, as amended,
29 U.S.C. § 2601 et seq.; the Fair Labor Standards Act of 1938, as amended, 29 U.S.C. § 201 et seq.; the Employee Retirement Income Security Act, as amended, 29 U.S.C.
§ 1001 et seq.; and the California Fair Employment and Housing Act, California Government Code Section 12940, et seq. 

Notwithstanding the generality of the foregoing, Executive does not release the following claims: 

(i)    Claims for unemployment compensation or any state disability insurance benefits pursuant to the
terms of applicable state law; 
 (ii)    Claims for workers’ compensation insurance benefits under
the terms of any worker’s compensation insurance policy or fund of the Company; 
 (iii)    Claims
pursuant to the terms and conditions of the federal law known as COBRA; 
 (iv)    Claims for indemnity
under the bylaws of the Company, as provided for by California law or under any applicable insurance policy with respect to Executive’s liability as an employee, director or officer of the Company; 

(v)    Claims based on any right Executive may have to enforce the Company’s executory obligations
under the Agreement; 
 (vi)    Executive’s right to bring to the attention of the Equal Employment
Opportunity Commission or the California Department of Fair Employment and Housing or any other federal, state or local government agency claims of discrimination, or from participating in an investigation or proceeding conducted by the Equal
Employment Opportunity Commission or any other federal, state or local government agency; provided, however, that Executive does release his right to secure any damages for alleged discriminatory treatment; 

(vii)    Claims Executive may have to vested or earned compensation and benefits; and 

(viii)    Executive’s right to communicate or cooperate with any governmental agency. 

  
 2 








 (b)    EXECUTIVE ACKNOWLEDGES THAT HE OR SHE HAS BEEN ADVISED OF AND IS
FAMILIAR WITH THE PROVISIONS OF CALIFORNIA CIVIL CODE SECTION 1542, WHICH PROVIDES 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.” 

BEING AWARE OF SAID CODE SECTION, EXECUTIVE HEREBY EXPRESSLY WAIVES ANY RIGHTS HE OR SHE MAY HAVE THEREUNDER, AS WELL AS UNDER ANY OTHER STATUTES OR COMMON LAW
PRINCIPLES OF SIMILAR EFFECT. 
 [Note: Clauses (c), (d) and (e) apply only if Executive is age 40 or older at time of
termination] 
 (c)    Executive acknowledges that this Release was presented to him or her on the date
indicated above and that Executive is entitled to have [twenty-one (21)][forty-five (45)] days’ time in which to consider it. Executive further acknowledges that the Company has advised him or her that he
or she is waiving his or her rights under the ADEA, and that Executive should consult with an attorney of his or her choice before signing this Release, and Executive has had sufficient time to consider the terms of this Release. Executive
represents and acknowledges that if Executive executes this Release before [twenty-one (21)][forty-five (45)] days have elapsed, Executive does so knowingly, voluntarily, and upon the advice and with the
approval of Executive’s legal counsel (if any), and that Executive voluntarily waives any remaining consideration period. 

(d)    Executive understands that after executing this Release, Executive has the right to revoke it within seven
(7) days after his or her execution of it. Executive understands that this Release will not become effective and enforceable unless the seven (7) day revocation period passes and Executive does not revoke the Release in writing. Executive
understands that this Release may not be revoked after the seven (7) day revocation period has passed. Executive also understands that any revocation of this Release must be made in writing and delivered to the Company at its principal place of
business within the seven (7) day period. 
 (e)    Executive understands that this Release shall become effective,
irrevocable, and binding upon Executive on the eighth (8th) day after his or her execution of it, so long as Executive has not revoked it within the time period and in the manner specified in
clause (d) above. 
 (f)    Executive further understands that Executive will not be given any severance benefits
under the Agreement unless this Release is effective on or before the date that is fifty-five (55) days following the date of Executive’s termination of employment. 

2.    No Assignment. Executive represents and warrants to the Company Releasees that there has been no assignment
or other transfer of any interest in any Claim that Executive may have against the Company Releasees. Executive agrees to indemnify and hold harmless the Company Releasees from any liability, claims, demands, damages, costs, expenses and
attorneys’ fees incurred as a result of any such assignment or transfer from Executive. 

  
 3 








 3.    Severability. In the event any provision of this Release is
found to be unenforceable by an arbitrator or court of competent jurisdiction, such provision shall be deemed modified to the extent necessary to allow enforceability of the provision as so limited, it being intended that the parties shall receive
the benefit contemplated herein to the fullest extent permitted by law. If a deemed modification is not satisfactory in the judgment of such arbitrator or court, the unenforceable provision shall be deemed deleted, and the validity and
enforceability of the remaining provisions shall not be affected thereby. 
 4.    Interpretation; Construction.
The headings set forth in this Release are for convenience only and shall not be used in interpreting this Agreement. This Release has been drafted by legal counsel representing the Company, but Executive has participated in the negotiation of its
terms. Furthermore, Executive acknowledges that Executive has had an opportunity to review and revise the Release and have it reviewed by legal counsel, if desired, and, therefore, 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 Release. Either party’s failure to enforce any provision of this Release shall not in any way be construed as a waiver of any such provision, or
prevent that party thereafter from enforcing each and every other provision of this Release. 
 5.    Governing Law
and Venue. This Release will be governed by and construed in accordance with the laws of the United States of America and the State of California applicable to contracts made and to be performed wholly within such State, and without regard to
the conflicts of laws principles thereof. Any suit brought hereon shall be brought in the state or federal courts sitting in San Diego County, California, the Parties hereby waiving any claim or defense that such forum is not convenient or proper.
Each party hereby agrees that any such court shall have in personam jurisdiction over it and consents to service of process in any manner authorized by California law. 

6.    Entire Agreement. This Release and the Agreement constitute the entire agreement of the Parties in respect of
the subject matter contained herein and therein and supersede all prior or simultaneous representations, discussions, negotiations and agreements, whether written or oral. This Release may be amended or modified only with the written consent of
Executive and an authorized representative of the Company. No oral waiver, amendment or modification will be effective under any circumstances whatsoever. 

7.    Counterparts. This Release may be executed in multiple counterparts, each of which shall be deemed to be an
original but all of which together shall constitute one and the same instrument. 
 (Signature Page Follows) 

  
 4 








 IN WITNESS WHEREOF, and intending to be legally bound, the Parties have executed the foregoing
Release as of the date first written above. 
  

			
	EXECUTIVE	  	CRINETICS PHARMACEUTICALS, INC.
		
	
                   
                                         
    
	  	By:                                     
                                         
    
		
	Print Name: R. Scott Struthers	  	Print Name:
		  	Title: