Document:

EX-10.1

 Exhibit 10.1 

INDEMNITY AGREEMENT 

THIS INDEMNITY AGREEMENT (this “Agreement”) dated
as of                              , 20    , is made by and between
METACRINE, INC., a Delaware corporation (the “Company”), and
                                        
 (“Indemnitee”). 
 RECITALS 

A.    The Company desires to attract and retain the services of highly qualified individuals as
directors, officers, employees and agents. 
 B.    The Company’s Amended and Restated
Bylaws (the “Bylaws”) require that the Company indemnify its directors and officers, and empowers the Company to indemnify its employees and other agents, as authorized by the Delaware General Corporation Law, as
amended (the “Code”), under which the Company is organized and such Bylaws expressly provide that the indemnification provided therein is not exclusive and contemplates that the Company may enter into separate agreements with
its directors, officers and other persons to set forth specific indemnification provisions. 

C.    Indemnitee does not regard the protection currently provided by applicable law, the Bylaws,
the Company’s other governing documents, and available insurance as adequate under the present circumstances, and the Company has determined that Indemnitee and other directors, officers, employees and agents of the Company may not be willing
to serve or continue to serve in such capacities without additional protection. 
 D.    The
Company desires and has requested Indemnitee to serve or continue to serve as a director, officer, employee or agent of the Company, as the case may be, and has proffered this Agreement to Indemnitee as an additional inducement to serve in such
capacity. 
 E.    Indemnitee is willing to serve, or to continue to serve, as a director,
officer, employee or agent of the Company, as the case may be, if Indemnitee is furnished the indemnity provided for herein by the Company. 

AGREEMENT 

NOW THEREFORE, in consideration of the mutual covenants and agreements set
forth herein, the parties hereto, intending to be legally bound, hereby agree as follows: 

1.    Definitions. 

(a)    Agent. For purposes of this Agreement, the term “Agent” of
the Company means any person who: (i) is or was a director, officer, employee, agent, or other fiduciary of the Company or a subsidiary of the Company; or (ii) is or was serving at the request or for the convenience of, or
representing the interests of, the Company or a subsidiary of the Company, as a director, officer, employee, agent, or other fiduciary of a foreign or domestic corporation, partnership, joint venture, trust or other enterprise. 

  
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 (b)    Change in Control. For purposes of this
Agreement, a “Change in Control” shall be deemed to have occurred if (i) any “person” (as such term is used in Sections 13(d) and 14(d) of the Securities Exchange Act of 1934, as amended (the
“Exchange Act”), other than a trustee or other fiduciary holding securities under an employee benefit plan of the Company or a corporation owned directly or indirectly by the stockholders of the Company in substantially the
same proportions as their ownership of stock of the Company, is or becomes the “beneficial owner” (as defined in Rule 13d-3 under the Exchange Act), directly or indirectly, of securities of the
Company representing 20% or more of the total voting power represented by the Company’s then outstanding Voting Securities, (ii) individuals who on the date of this Agreement are members of the Board (the “Incumbent
Board”) cease for any reason to constitute at least a majority of the members of the Board (provided, however, that if the appointment or election (or nomination for election) of any new Board member was approved or recommended
by a majority vote of the members of the Incumbent Board then still in office, such new member shall be considered as a member of the Incumbent Board), or (iii) the stockholders of the Company approve a merger or consolidation of the Company
with any other corporation, other than a merger or consolidation which would result in the Voting Securities of the Company outstanding immediately prior thereto continuing to represent (either by remaining outstanding or by being converted into
Voting Securities of the surviving entity) at least 80% of the total voting power represented by the Voting Securities of the Company or such surviving entity outstanding immediately after such merger or consolidation, or the stockholders of the
Company approve a plan of complete liquidation of the Company or an agreement for the sale or disposition by the Company of (in one transaction or a series of transactions) all or substantially all of the Company’s assets. 

(c)    Expenses. For purposes of this Agreement, the term “Expenses”
shall be broadly construed and shall include, without limitation, all direct and indirect costs of any type or nature whatsoever (including, without limitation, all attorneys’, witness, or other professional fees and related disbursements, and
other out-of-pocket costs of whatever nature, actually and reasonably incurred by Indemnitee in connection with the investigation, defense or appeal of a proceeding or
establishing or enforcing a right to indemnification under this Agreement, the Code or otherwise. The term “Expenses” shall also include reasonable compensation for time spent by Indemnitee for which he or she is not
compensated by the Company or any subsidiary or third party: (i) for any period during which Indemnitee is not an Agent, in the employment of, or providing services for compensation to, the Company or any subsidiary; and (ii) if the rate
of compensation and estimated time involved is approved by the directors of the Company who are not parties to any action with respect to which Expenses are incurred, for Indemnitee while an Agent of, employed by, or providing services for
compensation to, the Company or any subsidiary. 
 (d)    Independent Counsel. For
purposes of this Agreement, the term “Independent Counsel” means a law firm, or a partner (or, if applicable, member) of such a law firm, that is experienced in matters of corporation law and neither presently is, nor in the
past five (5) years has been, retained to represent: (i) the Company or Indemnitee in any matter material to either such party, or (ii) any other party to the proceeding giving rise to a claim for indemnification hereunder.
Notwithstanding the foregoing, the term “Independent Counsel” shall not include any person who, under the applicable standards of professional conduct then prevailing, would have a conflict of interest in representing either
the Company or Indemnitee in an action to determine Indemnitee’s rights under this Agreement. The Company will pay the reasonable fees and expenses of the Independent Counsel referred to above and to fully indemnify such counsel against any and

  
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all expenses, claims, liabilities and damages arising out of or relating to this Agreement or its engagement pursuant hereto. 

(e)    Liabilities. For purposes of this Agreement, the term
“Liabilities” shall be broadly construed and shall include, without limitation, judgments, damages, deficiencies, liabilities, losses, penalties, excise taxes, fines, assessments and amounts paid in settlement, including any
interest and any federal, state, local or foreign taxes imposed as a result of the actual or deemed receipt of any payment under this Agreement. 

(f)    Proceedings. For purposes of this Agreement, the term
“proceeding” shall be broadly construed and shall include, without limitation, any threatened, pending, or completed action, suit, claim, counterclaim, cross claim, arbitration, mediation, alternate dispute resolution
mechanism, investigation, inquiry, administrative hearing, or any other actual, threatened or completed proceeding, whether brought in the right of the Company or otherwise and whether of a civil, criminal, administrative or investigative nature,
and whether formal or informal in any case, in which Indemnitee was, is or will be involved as a party, potential party, non-party witness, or otherwise by reason of: (i) the fact that Indemnitee is or
was a director or officer of the Company; (ii) the fact that any action taken by Indemnitee (or a failure to take action by Indemnitee) or of any action (or failure to act) on Indemnitee’s part while acting as an Agent; or (iii) the
fact that Indemnitee is or was serving at the request of the Company as a director, officer, employee or agent of another corporation, partnership, joint venture, trust, employee benefit plan, or other enterprise, and in any such case described
above, whether or not serving in any such capacity at the time any liability or Expense is incurred for which indemnification, reimbursement, or advancement of Expenses may be provided under this Agreement. If the Indemnitee believes in good faith
that a given situation may lead to or culminate in the institution of a proceeding, this shall be considered a proceeding under this paragraph. 

(g)    Subsidiary. For purposes of this Agreement, the term
“subsidiary” means any corporation, limited liability company, or other entity, of which more than 50% of the outstanding voting securities or equity interests are owned, directly or indirectly, by the Company and one or more
of its subsidiaries, and any other corporation, limited liability company, partnership, joint venture, trust, employee benefit plan or other enterprise of which Indemnitee is or was serving at the request of the Company as an Agent. 

(h)    Voting Securities. For purposes of this Agreement, “Voting
Securities” shall mean any securities of the Company that vote generally in the election of directors. 

2.    Agreement to Serve. Indemnitee will serve, or continue to serve, as the case may be,
as an Agent, faithfully and to the best of his or her ability, at the will of such entity designated by the Company and at the request of the Company (or under separate agreement, if such agreement exists), in the capacity Indemnitee currently
serves such entity, so long as Indemnitee is duly appointed or elected and qualified in accordance with the applicable provisions of the governance documents of such entity, or until such time as Indemnitee tenders his or her resignation in writing;
provided, however, that nothing contained in this Agreement is intended as an employment agreement between Indemnitee and the Company or any of its subsidiaries or to create any right to continued employment of Indemnitee with the Company or any of
its subsidiaries in any capacity. 

  
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 The Company acknowledges that it has entered into this Agreement and assumes the
obligations imposed on it hereby, in addition to and separate from its obligations to Indemnitee under the Bylaws, to induce Indemnitee to serve, or continue to serve, as an Agent, and the Company acknowledges that Indemnitee is relying upon this
Agreement in serving as an Agent. 
 3.    Indemnification. 

(a)    Indemnification in Third Party Proceedings. Subject to Section 10 below, the
Company shall indemnify Indemnitee to the fullest extent permitted by the Code, as the same may be amended from time to time (but, to the fullest extent of the law, only to the extent that such amendment permits Indemnitee to broader indemnification
rights than the Code permitted prior to adoption of such amendment), if Indemnitee is a party to or threatened to be made a party to or otherwise involved in any proceeding, other than a proceeding by or in the right of the Company to procure a
judgment in its favor, for any and all Expenses and Liabilities (including all interest, assessments and other charges paid or payable in connection with or in respect of such Expenses and Liabilities) incurred by Indemnitee in connection with the
investigation, defense, settlement or appeal of such proceeding, if Indemnitee acted in good faith and in a manner Indemnitee reasonably believed to be in or not opposed to the best interests of the Company and, in the case of a criminal
proceeding had no reasonable cause to believe that Indemnitee’s conduct was unlawful. The parties hereto intend that this Agreement shall provide to the fullest extent permitted by law for indemnification in excess of that expressly permitted
by statute, including, without limitation, any indemnification provided by the Certificate of Incorporation of the Company, the Bylaws, vote of its stockholders or disinterested directors, or applicable law. 

(b)    Indemnification in Derivative Actions and Direct Actions by the Company. Subject to
Section 10 below, the Company shall indemnify Indemnitee to the fullest extent permitted by the Code, as the same may be amended from time to time (but, fullest extent permitted by applicable law, only to the extent that such amendment permits
Indemnitee to broader indemnification rights than the Code permitted prior to adoption of such amendment), if Indemnitee is a party to or threatened to be made a party to or otherwise involved in any proceeding by or in the right of the Company to
procure a judgment in its favor, against any and all Expenses actually and reasonably incurred by Indemnitee in connection with the investigation, defense, settlement, or appeal of such proceedings, if Indemnitee acted in good faith and in a manner
Indemnitee reasonably believed to be in or not opposed to the best interests of the Company. No indemnification for Expenses shall be made under this Section 3(b) in respect of any claim, issue or matter as to which Indemnitee shall have been
finally adjudged by a court competent jurisdiction to be liable to the Company, unless and only to the extent that the Chancery Court of the State of Delaware or any court in which the proceeding was brought shall determine upon application that,
despite the adjudication of liability but in view of all the circumstances of the case, Indemnitee is fairly and reasonably entitled to indemnification. 

4.    Indemnification of Expenses of Successful Party. Notwithstanding any other provision
of this Agreement, in circumstances where indemnification is not available under Section 3(a) or 3(b), as the case may be, to the fullest extent permitted by law and to the extent that Indemnitee is a party to (or a participant in) any
proceeding and has been successful on the merits or otherwise in defense of any proceeding or in defense of any claim, issue or matter therein, 

  
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in whole or part, including the dismissal of any action without prejudice, the Company shall indemnify Indemnitee against all Expenses and Liabilities in connection with the investigation,
defense or appeal of such proceeding. If Indemnitee is not wholly successful in such proceeding but is successful, on the merits or otherwise, as to one or more but less than all claims, issues or matters in such proceeding, the Company shall
indemnify Indemnitee against all Expenses and Liabilities incurred by Indemnitee or on Indemnitee’s behalf in connection with or related to each successfully resolved claim, issue or matter to the fullest extent permitted by law. 

5.    Partial Indemnification; Witness Indemnification. If Indemnitee is entitled under any
provision of this Agreement to indemnification by the Company for some or a portion of any Expenses and Liabilities incurred by Indemnitee in the investigation, defense, settlement or appeal of a proceeding, but is precluded by applicable law or the
specific terms of this Agreement to indemnification for the total amount thereof, the Company shall nevertheless indemnify Indemnitee for the portion thereof to which Indemnitee is entitled. Notwithstanding any other provision of this Agreement, to
the fullest extent permitted by applicable law and to the extent that Indemnitee is, by reason of Indemnitee’s acting as an Agent, a witness or otherwise asked to participate in any proceeding to which Indemnitee is not a party, Indemnitee
shall be indemnified against all Expenses incurred by Indemnitee or on Indemnitee’s behalf in connection therewith. 

6.    Advancement of Expenses. To the extent not prohibited by law, the Company shall
advance the Expenses incurred by Indemnitee in connection with any proceeding, and such advancement shall be made within twenty (20) days after the receipt by the Company of a statement or statements requesting such advances (which shall
include invoices received by Indemnitee in connection with such Expenses but, in the case of invoices in connection with legal services, any references to legal work performed or to expenditures made that would cause Indemnitee to waive any
privilege accorded by applicable law shall not be included with the invoice) and upon request of the Company, an undertaking to repay the advancement of Expenses if and to the extent that it is ultimately determined by a court of competent
jurisdiction in a final judgment, not subject to appeal, that Indemnitee is not entitled to be indemnified by the Company. Advances shall be unsecured, interest free and without regard to Indemnitee’s ability to repay the Expenses. Advances
shall include any and all Expenses incurred by Indemnitee pursuing an action to enforce Indemnitee’s right to indemnification under this Agreement or otherwise and this right of advancement, including expenses incurred preparing and forwarding
statements to the Company to support the advances claimed. Indemnitee acknowledges that the execution and delivery of this Agreement shall constitute an undertaking providing that Indemnitee shall, to the fullest extent required by law, repay the
advance (without interest) if and to the extent that it is ultimately determined by a court of competent jurisdiction in a final judgment, not subject to appeal, that Indemnitee is not entitled to be indemnified by the Company. The right to advances
under this Section shall continue until final disposition of any proceeding, including any appeal therein. This Section 6 shall not apply to any claim made by Indemnitee for which indemnity is excluded pursuant to Section 10(b). 

7.    Notice and Other Indemnification Procedures. 

(a)    Notification of Proceeding. Indemnitee will notify the Company in writing promptly
upon being served with any summons, citation, subpoena, complaint, indictment, information or other document relating to any proceeding or matter which may be subject to 

  
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indemnification or advancement of Expenses covered hereunder. The written notification to the Company shall include a description of the nature of the proceeding and the facts underlying the
proceeding. The failure of Indemnitee to so notify the Company shall not relieve the Company of any obligation which it may have to Indemnitee under this Agreement or otherwise and any delay in so notifying the Company shall not constitute a waiver
by Indemnitee of any rights under this Agreement. 
 (b)    Request for Indemnification
Payments. To obtain indemnification under this Agreement, Indemnitee shall submit to the Company a written request, including therein or therewith such documentation and information as is reasonably available to Indemnitee and is reasonably
necessary to determine whether and to what extent Indemnitee is entitled to indemnification under the terms of this Agreement, and shall request payment thereof by the Company. 

(c)    Determination of Right to Indemnification Payments. Upon written request by
Indemnitee for indemnification pursuant to the Section 7(b) hereof, a determination with respect to Indemnitee’s entitlement thereto shall be made in the specific case by one of the following four methods, which shall be at the election of
the Board of Directors: (1) by a majority vote of the disinterested directors, even though less than a quorum, (2) by a committee of disinterested directors designated by a majority vote of the disinterested directors, even though less
than a quorum, (3) if there are no disinterested directors or if the disinterested directors so direct, by Independent Counsel in a written opinion to the Board of Directors, a copy of which shall be delivered to the Indemnitee, or (4) if
so directed by the Board of Directors, by the stockholders of the Company; provided, however, that if there has been a Change in Control, then such determination shall be made by Independent Counsel selected by Indemnitee and approved by the
Company (which approval shall not be unreasonably withheld). For purposes hereof, disinterested directors are those members of the board of directors of the Company who are not parties to the action, suit or proceeding in respect of which
indemnification is sought by Indemnitee. Indemnification payments requested by Indemnitee under Section 3 hereof shall be made by the Company no later than sixty (60) days after receipt of the written request of Indemnitee. Claims for
advancement of Expenses shall be made under the provisions of Section 6 herein. 

(d)    Application for Enforcement. In the event the Company fails to make timely payments
as set forth in Sections 6 or 7(b) above, Indemnitee shall have the right to apply to any court of competent jurisdiction for the purpose of enforcing Indemnitee’s right to indemnification or advancement of Expenses pursuant to this Agreement.
In such an enforcement hearing or proceeding, the burden of proof shall be on the Company to prove that indemnification or advancement of Expenses to Indemnitee is not required under this Agreement or permitted by applicable law. Any determination
by the Company (including its Board of Directors, a committee thereof, Independent Counsel) or stockholders of the Company, that Indemnitee is not entitled to indemnification hereunder, shall not be a defense by the Company to the action nor create
any presumption that Indemnitee is not entitled to indemnification or advancement of Expenses hereunder. 

(e)    Indemnification of Certain Expenses. The Company shall indemnify Indemnitee against
all Expenses incurred in connection with any hearing or proceeding under this 

  
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Section 7 unless the Company prevails in such hearing or proceeding on the merits in all material respects. 

8.    Assumption of Defense. In the event the Company shall be requested by Indemnitee to
pay the Expenses of any proceeding, the Company, if appropriate, shall be entitled to assume the defense of such proceeding, or to participate to the extent permissible in such proceeding, with counsel reasonably acceptable to Indemnitee. Upon
assumption of the defense by the Company and the retention of such counsel by the Company, the Company shall not be liable to Indemnitee under this Agreement for any fees of counsel subsequently incurred by Indemnitee with respect to the same
proceeding, provided that Indemnitee shall have the right to employ separate counsel in such proceeding at Indemnitee’s sole cost and expense. Notwithstanding the foregoing, if Indemnitee’s counsel delivers a written notice to the Company
stating that such counsel has reasonably concluded that there may be a conflict of interest between the Company and Indemnitee in the conduct of any such defense or the Company shall not, in fact, have employed counsel or otherwise actively pursued
the defense of such proceeding within a reasonable time, then in any such event the fees and Expenses of Indemnitee’s counsel to defend such proceeding shall be subject to the indemnification and advancement of Expenses provisions of this
Agreement. 
 9.    Insurance. To the extent that the Company maintains an insurance policy or
policies providing liability insurance for Agents (“D&O Insurance”), Indemnitee shall be covered by such policy or policies in accordance with its or their terms to the maximum extent of the coverage available for
any such Agent under such policy or policies. If, at the time of the receipt of a notice of a claim pursuant to the terms hereof, the Company has D&O Insurance in effect or otherwise potentially available, the Company shall give prompt
notice of the commencement of such proceeding to the insurers in accordance with the procedures set forth in the respective policies. The Company shall thereafter take all necessary or desirable action to cause such insurers to pay, on behalf of
Indemnitee, all amounts payable as a result of such proceeding in accordance with the terms of such policies. 

10.    Exceptions. 

(a)    Certain Matters. Any provision herein to the contrary notwithstanding, the Company
shall not be obligated pursuant to the terms of this Agreement to indemnify Indemnitee on account of any proceeding with respect to: (i) remuneration paid to Indemnitee if it is determined by final judgment or other final adjudication that such
remuneration was in violation of law (and, in this respect, both the Company and Indemnitee have been advised that the Securities and Exchange Commission believes that indemnification for liabilities arising under the federal securities laws is
against public policy and is, therefore, unenforceable and that claims for indemnification should be submitted to appropriate courts for adjudication, as indicated in Section 10(d) below); (ii) a final judgment rendered against Indemnitee
for an accounting, disgorgement or repayment of profits made from the purchase or sale by Indemnitee of securities of the Company against Indemnitee or in connection with a settlement by or on behalf of Indemnitee to the extent it is acknowledged by
Indemnitee and the Company that such amount paid in settlement resulted from Indemnitee’s conduct from which Indemnitee received monetary personal profit, pursuant to the provisions of Section 16(b) of the Exchange Act or other provisions
of any federal, state or local statute or rules and regulations thereunder; (iii) a final judgment or other final adjudication 

  
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that Indemnitee’s conduct was in bad faith, knowingly fraudulent or deliberately dishonest or constituted willful misconduct (but only to the extent of such specific determination); or
(iv) on account of conduct that is established by a final judgment as constituting a breach of Indemnitee’s duty of loyalty to the Company or resulting in any personal profit or advantage to which Indemnitee is not legally entitled. For
purposes of the foregoing sentence, a final judgment or other adjudication may be reached in either the underlying proceeding or action in connection with which indemnification is sought or a separate proceeding or action to establish rights and
liabilities under this Agreement. 
 (b)    Claims Initiated by Indemnitee. Any provision
herein to the contrary notwithstanding, the Company shall not be obligated to indemnify or advance Expenses to Indemnitee with respect to proceedings or claims initiated or brought by Indemnitee against the Company or its Agents and not by way of
defense, except (i) with respect to proceedings brought to establish or enforce a right to indemnification or advancement under this Agreement or under any other agreement, provision in the Bylaws or the Certificate of Incorporation or
applicable law, or (ii) with respect to any other proceeding initiated by Indemnitee that is either approved by the Board of Directors or Indemnitee’s participation is required by applicable law. However, indemnification or advancement of
Expenses may be provided by the Company in specific cases if the Board of Directors determines it to be appropriate. 

(c)    Unauthorized Settlements. Any provision herein to the contrary notwithstanding, the
Company shall not be obligated pursuant to the terms of this Agreement to indemnify Indemnitee under this Agreement for any amounts paid in settlement of a proceeding effected without the Company’s written consent. Neither the Company nor
Indemnitee shall unreasonably withhold consent to any proposed settlement; provided, however, that the Company may in any event decline to consent to (or to otherwise admit or agree to any liability for indemnification hereunder in respect of) any
proposed settlement if the Company is also a party in such proceeding and determines in good faith that such settlement is not in the best interests of the Company and its stockholders. 

(d)    Securities Act Liabilities. Any provision herein to the contrary notwithstanding, the
Company shall not be obligated pursuant to the terms of this Agreement to indemnify Indemnitee or otherwise act in violation of any undertaking appearing in and required by the rules and regulations promulgated under the Securities Act of 1933, as
amended (the “Securities Act”), or in any registration statement filed with the SEC under the Securities Act. Indemnitee acknowledges that paragraph (h) of Item 512 of Regulation S-K currently generally requires the Company to undertake in connection with any registration statement filed under the Securities Act to submit the issue of the enforceability of Indemnitee’s rights under this
Agreement in connection with any liability under the Securities Act on public policy grounds to a court of appropriate jurisdiction and to be governed by any final adjudication of such issue. Indemnitee specifically agrees that any such undertaking
shall supersede the provisions of this Agreement and to be bound by any such undertaking. 

(e)    Prior Payments Any provision herein to the contrary notwithstanding, the Company
shall not be obligated pursuant to the terms of this Agreement to indemnify or advance Expenses to Indemnitee under this Agreement for which payment has actually been made to or on 

  
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behalf of Indemnitee under any insurance policy or other indemnity provision, expect with respect to any excess beyond the amount paid under any insurance policy or indemnity policy. 

11.    Nonexclusivity and Survival of Rights. The provisions for indemnification and
advancement of Expenses set forth in this Agreement shall not be deemed exclusive of any other rights which Indemnitee may at any time be entitled under any provision of applicable law, the Company’s Certificate of Incorporation, the Bylaws or
other agreements, both as to action in Indemnitee’s official capacity and Indemnitee’s action as an Agent, in any court in which a proceeding is brought, and Indemnitee’s rights hereunder shall continue after Indemnitee has ceased
acting as an Agent and shall inure to the benefit of the heirs, executors, administrators and assigns of Indemnitee. The obligations and duties of the Company to Indemnitee under this Agreement shall be binding on the Company and its successors and
assigns until terminated in accordance with its terms. The Company shall require any successor (whether direct or indirect, by purchase, merger, consolidation or otherwise) to all or substantially all of the business or assets of the Company,
expressly to assume and agree to perform this Agreement in the same manner and to the same extent that the Company would be required to perform if no such succession had taken place. 

No amendment, alteration or repeal of this Agreement or of any provision hereof shall limit or restrict any right of
Indemnitee under this Agreement in respect of any action taken or omitted by such Indemnitee in his or her corporate status prior to such amendment, alteration or repeal. To the extent that a change in the Code, whether by statute or judicial
decision, permits greater indemnification or advancement of Expenses than would be afforded currently under the Company’s Certificate of Incorporation, the Bylaws and this Agreement, it is the intent of the parties hereto that Indemnitee shall
enjoy by this Agreement the greater benefits so afforded by such change. No right or remedy herein conferred is intended to be exclusive of any other right or remedy, and every other right and remedy shall be cumulative and in addition to every
other right and remedy given hereunder or now or hereafter existing at law or in equity or otherwise. The assertion or employment of any right or remedy hereunder, or otherwise, by Indemnitee shall not prevent the concurrent assertion or employment
of any other right or remedy by Indemnitee. 
 12.    Term. This Agreement shall continue
until and terminate upon the later of: (a) five (5) years after the date that Indemnitee shall have ceased to serve as an Agent; or (b) one (1) year after the final termination of any proceeding, including any appeal then pending, in
respect to which Indemnitee was granted rights of indemnification or advancement of Expenses hereunder. 
 No legal action
shall be brought and no cause of action shall be asserted by or in the right of the Company against an Indemnitee or an Indemnitee’s estate, spouse, heirs, executors or personal or legal representatives after the expiration of five
(5) years from the date of accrual of such cause of action, and any claim or cause of action of the Company shall be extinguished and deemed released unless asserted by the timely filing of a legal action within such five-year period; provided,
however, that if any shorter period of limitations is otherwise applicable to such cause of action, such shorter period shall govern. 

13.    Subrogation. In the event of payment under this Agreement, the Company shall be
subrogated to the extent of such payment to all of the rights of recovery of Indemnitee, who, at the request and expense of the Company, shall execute all papers required and shall do everything that

  
 9. 

 
may be reasonably necessary to secure such rights, including the execution of such documents necessary to enable the Company effectively to bring suit to enforce such rights. 

14.    Interpretation of Agreement. It is understood that the parties hereto intend this
Agreement to be interpreted and enforced so as to provide indemnification and advancement of Expenses to Indemnitee to the fullest extent now or hereafter permitted by law. 

15.    Severability. If any provision of this Agreement shall be held to be invalid, illegal
or unenforceable for any reason whatsoever, (a) the validity, legality and enforceability of the remaining provisions of the Agreement (including without limitation, all portions of any paragraphs of this Agreement containing any such provision
held to be invalid, illegal or unenforceable, that are not themselves invalid, illegal or unenforceable) shall not in any way be affected or impaired thereby; and (b) to the fullest extent possible, the provisions of this Agreement (including,
without limitation, all portions of any paragraph of this Agreement containing any such provision held to be invalid, illegal or unenforceable, that are not themselves invalid, illegal or unenforceable) shall be construed so as to give effect to the
intent manifested by the provision held invalid, illegal or unenforceable and to give effect to Section 14 hereof. 

16.    Amendment and Waiver. No supplement, modification, amendment, or cancellation of this
Agreement shall be binding unless executed in writing by the parties hereto. No waiver of any of the provisions of this Agreement shall be deemed or shall constitute a waiver of any other provision hereof (whether or not similar) nor shall such
waiver constitute a continuing waiver. 
 17.    Notice. Except as otherwise provided
herein, any notice or demand which, by the provisions hereof, is required or which may be given to or served upon the parties hereto shall be in writing and, if by electronic transmission, shall be deemed to have been validly served, given or
delivered when sent, if by overnight delivery, courier or personal delivery, shall be deemed to have been validly served, given or delivered upon actual delivery and, if mailed, shall be deemed to have been validly served, given or delivered three
(3) business days after deposit in the United States mail, as registered or certified mail, with proper postage prepaid and addressed to the party or parties to be notified at the addresses set forth on the signature page of this Agreement (or
such other address(es) as a party may designate for itself by like notice). If to the Company, notices and demands shall be delivered to the attention of the Secretary of the Company. 

18.    Governing Law. This Agreement shall be governed exclusively by and construed
according to the laws of the State of Delaware, as applied to contracts between Delaware residents entered into and to be performed entirely within Delaware. 

19.    Counterparts. This Agreement may be executed in one or more counterparts, each of
which shall for all purposes be deemed to be an original but all of which together shall constitute but one and the same Agreement. Only one such counterpart need be produced to evidence the existence of this Agreement. 

20.    Headings. The headings of the sections of this Agreement are inserted for convenience
only and shall not be deemed to constitute part of this Agreement or to affect the construction hereof. 

  
 10. 

 21.    Entire Agreement. Subject to
Section 11 hereof, this Agreement constitutes the entire agreement between the parties with respect to the subject matter hereof and supersedes all prior agreements, understandings and negotiations, written and oral, between the parties with
respect to the subject matter of this Agreement; provided, however, that this Agreement is a supplement to and in furtherance of the Company’s Certificate of Incorporation, the Bylaws, the Code and any other applicable law, and shall not be
deemed a substitute therefor, and does not diminish or abrogate any rights of Indemnitee thereunder. 

22.    Contribution. To the fullest extent permissible under applicable law, if the
indemnification provided for in this Agreement is unavailable to Indemnitee for any reason whatsoever, the Company, in lieu of indemnifying Indemnitee, shall contribute to the amount incurred by Indemnitee, whether for judgments, fines, penalties,
excise taxes, amounts paid or to be paid in settlement and/or for Expenses, in connection with any claim relating to an indemnifiable event under this Agreement, in such proportion as is deemed fair and reasonable in light of all of the
circumstances of such proceeding in order to reflect (i) the relative benefits received by the Company and Indemnitee as a result of the event(s) and/or transaction(s) giving cause to such proceeding; and/or (ii) the relative fault of the
Company and Indemnitee in connection with such event(s) and/or transaction(s). 

23.    Consent to Jurisdiction. The Company and Indemnitee hereby irrevocably and
unconditionally (i) agree that any action or proceeding arising out of or in connection with this Agreement shall be brought only in the Chancery Court of the State of Delaware (the “Delaware Court”), and not in any
other state or federal court in the United States of America or any court in any other country, (ii) consent to submit to the exclusive jurisdiction of the Delaware Court for purposes of any action or proceeding arising out of or in connection
with this Agreement, (iii) agree to appoint, to the extent such party is not otherwise subject to service of process in the State of Delaware, an agent in the State of Delaware as such party’s agent for acceptance of legal process in
connection with any such action or proceeding against such party with the same legal force and validity as if served upon such party personally within the State of Delaware, (iv) waive any objection to the laying of venue of any such action or
proceeding in the Delaware Court, and (v) waive, and agree not to plead or to make, any claim that any such action or proceeding brought in the Delaware Court has been brought in an improper or inconvenient forum. 

  
 11. 

 IN WITNESS
WHEREOF, the parties hereto have entered into this Agreement effective as of the date first above written. 
  

					
	METACRINE, INC.
		
	By:	 	 
		 	Name:	 	 
		 	Title:	 	 
	
	INDEMNITEE
	
	 
	Signature of Indemnitee
	
	 
	Print or Type Name of IndemniteeEX-10.6

 Exhibit 10.6 

METACRINE, INC. 

SEVERANCE BENEFIT PLAN 

APPROVED BY THE BOARD OF DIRECTORS
ON AUGUST 9, 2018 
 Section 1.    INTRODUCTION. 

The Metacrine, Inc. Severance Benefit Plan (the “Plan”) is hereby established effective upon the date
of approval by the Board of Directors of Metacrine, Inc. (the “Company”) set forth above (the “Effective Date”). The purpose of the Plan is to provide for the payment of severance benefits to
eligible employees of the Company in the event that such employees become subject to involuntary or constructive employment terminations. This Plan document also is the Summary Plan Description for the Plan. 

For purposes of the Plan, the following terms are defined as follows: 

(a)    “Affiliate” means any corporation (other than the Company) in an
“unbroken chain of corporations” beginning with the Company, if each of the corporations other than the last corporation in the unbroken chain owns stock possessing 50% or more of the total combined voting power of all classes of stock in
one of the other corporations in such chain. 
 (b)     “Base Salary”
means base pay (excluding incentive pay, premium pay, commissions, overtime, bonuses and other forms of variable compensation) as in effect prior to any reduction that would give rise to an employee’s right to a resignation for Good Reason (if
applicable). 
 (c)    “Cause” means, with respect to a particular
employee, the meaning ascribed to such term in any written employment agreement, offer letter or similar agreement between such employee and the Company defining such term, and, in the absence of such agreement, means with respect to such employee,
the occurrence of any of the following events: (i) such employee’s commission of any felony or any crime involving fraud, dishonesty or moral turpitude under the laws of the United States or any state thereof; (ii) such
employee’s attempted commission of, or participation in, a fraud or act of dishonesty against the Company; (iii) such employee’s intentional, material violation of any contract or agreement between the employee and the Company or of
any statutory duty owed to the Company; (iv) such employee’s unauthorized use or disclosure of the Company’s confidential information or trade secrets; or (v) such employee’s gross misconduct. The determination whether a
termination is for Cause shall be made by the Plan Administrator in its sole and exclusive judgment and discretion. 

(d)    “Change in Control” has the meaning ascribed to such term in the
Equity Plan. 
 (e)    “Change in Control Period” means the period
commencing three months prior to the Closing of a Change in Control and ending 12 months following the Closing of a Change in Control. 

(f)    “Closing” means the initial closing of the Change in Control as
defined in the definitive agreement executed in connection with the Change in Control. In the case of a series 
  

 of transactions constituting a Change in Control, “Closing” means the first closing
that satisfies the threshold of the definition for a Change in Control. 

(g)    “Code” means the Internal Revenue Code of 1986, as amended,
including any applicable regulations and guidance thereunder. 

(h)    “Committee” means the Board of Directors or the Compensation
Committee of the Board of Directors of the Company. 
 (i)    “Company”
means Metacrine, Inc. or, following a Change in Control, the surviving entity resulting from such event. 

(j)    “Covered Termination” means a termination of employment that is due
to (1) a termination by the Company without Cause (and other than as a result of the employee’s death or Disability) or (2) an employee’s resignation for Good Reason. 

(k)    “Director” means a member of the Board of Directors of the Company.

 (l)    “Disability” means any physical or mental condition which
renders an employee incapable of performing the work for which he or she was employed by the Company or similar work offered by the Company. The Disability of an employee shall be established if (i) the employee satisfies the requirements
for benefits under the Company’s long-term disability plan or (ii) if no long-term disability plan, the employee satisfies the requirements for Social Security disability benefits. 

(m)     “Eligible Employee” means an employee of the Company that meets the
requirements to be eligible to receive Plan benefits as set forth in Section 2. 

(n)    “Equity Plan” means the Metacrine, Inc. Amended and Restated 2015
Equity Incentive Plan, as amended from time to time; provided that, upon and following the IPO Date, the “Equity Plan” means the Metacrine, Inc. 2018 Equity Incentive Plan, as amended from time to time. 

(o)    “Good Reason” for an employee’s resignation means the
occurrence of any one or more of the following are undertaken by the Company (or successor to the Company, if applicable) without the employee’s express written consent: (i) a material reduction in a such employee’s annual base
salary; provided, however, that Good Reason will not be deemed to have occurred in the event of a reduction in such employee’s annual base salary that is pursuant to a salary reduction program affecting substantially all of the employees
of the Company and that does not adversely affect such employee to a greater extent than other similarly situated employees; (ii) a material reduction in such employee’s authority, duties or responsibilities; provided, however, that
a change in job position (including a change in title) shall not be deemed a “material reduction” in and of itself unless the employee’s new duties are materially reduced from the employee’s prior duties; (iii) a relocation
of such employee’s principal place of employment with the Company (or successor to the Company, if applicable) to a place that increases such employee’s one-way commute by more than 50 miles as
compared to such employee’s then-current principal place of employment immediately prior to such relocation, except for required travel by the employee on the Company’s business to an extent substantially consistent with employee’s
business travel 

  
 2. 

 
obligations prior to the effective date of the Change in Control; or (iv) a material breach by the Company of any provision of this Plan or any other material agreement between such employee
and the Company concerning the terms and conditions of such employee’s employment or service with the Company, provided, however, that in each case (i) through (iv) above, in order for the employee’s resignation to be deemed to
have been for Good Reason, the employee must first give the Company written notice of the action or omission giving rise to “Good Reason” within 30 days after the first occurrence thereof; the Company must fail to reasonably cure such
action or omission within 30 days after receipt of such notice (the “Cure Period”), and the employee’s resignation must be effective not later than 30 days after the expiration of such Cure Period. 

(p)    “IPO Date” means the date of the underwriting agreement between the
Company and the underwriter(s) managing the initial public offering of the Company’s Common Stock, pursuant to which the Common Stock is priced for the initial public offering. 

(q)    “Participation Agreement” means an agreement between an employee and
the Company in substantially the form of APPENDIX A attached hereto, and which may include such other terms as the Committee deems necessary or advisable in the administration of the Plan. 

(r)    “Plan Administrator” means the Committee prior to the Closing and
the Representative upon and following the Closing, as applicable. 

(s)    “Representative” means one or more members of the Committee or other
persons or entities designated by the Committee prior to or in connection with a Change in Control that will have authority to administer and interpret the Plan upon and following the Closing as provided in Section 8(a). 

(t)    “Section 409A” means
Section 409A of the Code and any state law of similar effect. 
 Section 2.    ELIGIBILITY
FOR BENEFITS. 
 (a)    Eligible Employee. Each employee
of the Company is eligible to participate in the Plan provided (i) such employee has signed and returned such Participation Agreement to the Company within 30 days following the date on which it is first provided to such employee; and
(ii) such employee meets the other Plan eligibility requirements set forth in this Section 2. The determination of whether an employee is an Eligible Employee shall be made by the Plan Administrator, in its sole discretion, and such
determination shall be binding and conclusive on all persons. 
 (b)    Release
Requirement. Except as otherwise provided in an individual Participation Agreement, in order to be eligible to receive benefits under the Plan, the employee also must execute a general waiver and release, in such a form as provided by the
Company (the “Release”), within the applicable time period set forth therein, and such Release must become effective in accordance with its terms, which must occur in no event more than 60 days following the date of the
applicable Covered Termination. 
 (c)    Plan Benefits Provided In Lieu of Individual
Agreement Benefits. This Plan shall supersede any change in control or severance benefit plan, policy or practice previously 

  
 3. 

 
maintained by the Company with respect to an Eligible Employee and any change in control or severance benefits in any individually negotiated employment contract or other agreement between the
Company and an Eligible Employee, with the exception of any provisions contained in any employment contract or option or stock award agreement between the Company and an Eligible Employee or any equity incentive plan, stock or option award agreement
or other change in control or severance plan maintained by the Company and applicable to such Eligible Employee (an “Individual Agreement”) that would provide more advantageous benefits to the Eligible Employee, in which
case, the Eligible Employee shall be eligible for the benefits under both this Plan and the Individual Agreement, to the extent such benefits in the Individual Agreement are not duplicative of the benefits under this Plan. 

(d)    Exceptions to Severance Benefit Entitlement. An employee who otherwise is an Eligible
Employee will not receive severance benefits under the Plan in the following circumstances, as determined by the Plan Administrator in its sole discretion: 

(1)    The employee is terminated by the Company for any reason (including due to the
employee’s death or disability) or voluntarily terminates employment with the Company in any manner, and in either case, such termination does not constitute a Covered Termination. Voluntary terminations include, but are not limited to,
resignation, retirement or failure to return from a leave of absence on the scheduled date. 

(2)    The employee voluntarily terminates employment with the Company in order to accept
employment with another entity that is wholly or partly owned (directly or indirectly) by the Company or an Affiliate. 

(3)    The employee is offered an identical or substantially equivalent or comparable position
with the Company or an Affiliate. For purposes of the foregoing, a “substantially equivalent or comparable position” is one that provides the employee substantially the same level of responsibility and compensation and would not give rise
to the employee’s right to a resignation for Good Reason. 
 (4)    The employee is offered
immediate reemployment by a successor to the Company or an Affiliate or by a purchaser of the Company’s assets, as the case may be, following a Change in Control and the terms of such reemployment would not give rise to the employee’s
right to a resignation for Good Reason. For purposes of the foregoing, “immediate reemployment” means that the employee’s employment with the successor to the Company or an Affiliate or the purchaser of its assets, as the case
may be, results in uninterrupted employment such that the employee does not incur a lapse in pay or benefits as a result of the change in ownership of the Company or the sale of its assets. For the avoidance of doubt, an employee who becomes
immediately reemployed as described in this Section 2(d)(4) by a successor to the Company or an Affiliate or by a purchaser of the Company’s assets, as the case may be, following a Change in Control shall continue to be an Eligible
Employee following the date of such reemployment. 
 (5)    The employee is rehired by the
Company or an Affiliate and recommences employment prior to the date severance benefits under the Plan are scheduled to commence. 

  
 4. 

 (e)    Termination or Reduction of Severance
Benefits. An Eligible Employee’s right to receive severance benefits under this Plan shall terminate immediately if, at any time prior to or during the period for which the Eligible Employee is receiving severance benefits under the Plan,
the Eligible Employee, without the prior written approval of the Plan Administrator willfully breaches any material statutory, common law, or contractual obligation to the Company or an Affiliate (including, without limitation, the contractual
obligations set forth in any confidentiality, non-disclosure and developments agreement, non-competition, non-solicitation, or
similar type agreement between the Eligible Employee and the Company, as applicable). 
 Section 3.    AMOUNT
OF BENEFITS. 
 (a)    Benefits in Participation Agreement.
Benefits under the Plan shall be provided to an Eligible Employee as set forth in the Participation Agreement. 

(b)    Additional Benefits. Notwithstanding the foregoing, the Company may, in its sole
discretion, provide benefits to individuals who are not Eligible Employees (“Non-Eligible Employees”) chosen by the Plan Administrator, in its sole discretion, and the provision of any
such benefits to a Non-Eligible Employee shall in no way obligate the Company to provide such benefits to any other individual, even if similarly situated. If benefits under the Plan are provided to a Non-Eligible Employee, references in the Plan to “Eligible Employee” (and similar references) shall be deemed to refer to such Non-Eligible Employee. 

(c)    Certain Reductions. In addition to Section 2(e) above, the Company, in its sole
discretion, shall have the authority to reduce an Eligible Employee’s severance benefits, in whole or in part, by any other severance benefits, pay and benefits provided during a period following written notice of a business closing or mass
layoff, pay and benefits in lieu of such notice, or other similar benefits payable to the Eligible Employee by the Company or an Affiliate that become payable in connection with the Eligible Employee’s termination of employment pursuant to
(i) any applicable legal requirement, including, without limitation, the Worker Adjustment and Retraining Notification Act or any other similar state law or (ii) any Company policy or practice providing for the Eligible Employee to remain
on the payroll for a limited period of time after being given notice of the termination of the Eligible Employee’s employment, and the Plan Administrator shall so construe and implement the terms of the Plan. Any such reductions that the
Company determines to make pursuant to this Section 3(c) shall be made such that any severance benefit under the Plan shall be reduced solely by any similar type of benefit under such legal requirement, agreement, policy or practice
(i.e., any cash severance benefits under the Plan shall be reduced solely by any cash payments or severance benefits under such legal requirement, agreement, policy or practice). The Company’s decision to apply such reductions to the
severance benefits of one Eligible Employee and the amount of such reductions shall in no way obligate the Company to apply the same reductions in the same amounts to the severance benefits of any other Eligible Employee. In the Company’s sole
discretion, such reductions may be applied on a retroactive basis, with severance benefits previously paid being re-characterized as payments pursuant to the Company’s statutory obligation. 

(d)    Parachute Payments. If any payment or benefit an Eligible Employee will or may
receive from the Company or otherwise (a “Payment”) would (i) constitute a “parachute 

  
 5. 

 
payment” within the meaning of Section 280G of the Code, and (ii) but for this sentence, be subject to the excise tax imposed by Section 4999 of the Code (the
“Excise Tax”), then any such Payment shall be equal to the Reduced Amount. The “Reduced Amount” shall be either (x) the largest portion of the Payment that would result in no portion of the
Payment (after reduction) being subject to the Excise Tax or (y) the largest portion, up to and including the total, of the Payment, whichever amount (i.e., the amount determined by clause (x) or by clause (y)), after taking into account
all applicable federal, state and local employment taxes, income taxes, and the Excise Tax (all computed at the highest applicable marginal rate), results in the Eligible Employee’s receipt, on an
after-tax basis, of the greater economic benefit notwithstanding that all or some portion of the Payment may be subject to the Excise Tax. If a reduction in a Payment is required pursuant to the preceding
sentence and the Reduced Amount is determined pursuant to clause (x) of the preceding sentence, the reduction shall occur in the manner (the “Reduction Method”) that results in the greatest economic benefit for the
Eligible Employee. If more than one method of reduction will result in the same economic benefit, the items so reduced will be reduced pro rata (the “Pro Rata Reduction Method”). 

Notwithstanding any provisions in this Section above to the contrary, if the Reduction Method or the Pro Rata Reduction Method
would result in any portion of the Payment being subject to taxes pursuant to Section 409A that would not otherwise be subject to taxes pursuant to Section 409A, then the Reduction Method and/or the Pro Rata Reduction Method, as the case
may be, shall be modified so as to avoid the imposition of taxes pursuant to Section 409A as follows: (A) as a first priority, the modification shall preserve to the greatest extent possible, the greatest economic benefit for the Eligible
Employee as determined on an after-tax basis; (B) as a second priority, Payments that are contingent on future events (e.g., being terminated without Cause), shall be reduced (or eliminated) before
Payments that are not contingent on future events; and (C) as a third priority, Payments that are “deferred compensation” within the meaning of Section 409A shall be reduced (or eliminated) before Payments that are not deferred
compensation within the meaning of Section 409A. 
 The Company shall appoint a nationally recognized accounting or law
firm to make the determinations required by this Section. The Company shall bear all expenses with respect to the determinations by such accounting or law firm required to be made hereunder. The Company shall use commercially reasonable efforts to
cause the accounting or law firm engaged to make the determinations hereunder to provide its calculations, together with detailed supporting documentation, to Eligible Employee and the Company within 15 calendar days after the date on which Eligible
Employee’s right to a Payment becomes reasonably likely to occur (if requested at that time by Eligible Employee or the Company) or such other time as requested by Eligible Employee or the Company. 

If the Eligible Employee receives a Payment for which the Reduced Amount was determined pursuant to clause (x) above and
the Internal Revenue Service determines thereafter that some portion of the Payment is subject to the Excise Tax, Eligible Employee agrees to promptly return to the Company a sufficient amount of the Payment (after reduction pursuant to clause
(x) above) so that no portion of the remaining Payment is subject to the Excise Tax. For the avoidance of doubt, if the Reduced Amount was determined pursuant to clause (y) above, the Eligible Employee shall have no obligation to return
any portion of the Payment pursuant to the preceding sentence. 

  
 6. 

 Section 4.    RETURN OF COMPANY
PROPERTY. 
 An Eligible Employee will not be entitled to any severance benefit under the Plan unless and
until the Eligible Employee returns all Company Property. For this purpose, “Company Property” means all Company documents (and all copies thereof) and other Company property which the Eligible Employee had in his or her
possession at any time, including, but not limited to, Company files, notes, drawings, records, plans, forecasts, reports, studies, analyses, proposals, agreements, financial information, research and development information, sales and marketing
information, operational and personnel information, specifications, code, software, databases, computer-recorded information, tangible property and equipment (including, but not limited to, computers, facsimile machines, mobile telephones, servers),
credit cards, entry cards, identification badges and keys; and any materials of any kind which contain or embody any proprietary or confidential information of the Company (and all reproductions thereof in whole or in part). 

Section 5.    TIME OF PAYMENT AND FORM
OF BENEFITS. 
 The Company reserves the right in the Participation Agreement to specify
whether payments under the Plan will be paid in a single sum, in installments, or in any other form and to determine the timing of such payments. All such payments under the Plan will be subject to applicable withholding for federal, state and local
taxes. All benefits provided under the Plan are intended to satisfy the requirements for an exemption from application of Section 409A to the maximum extent that an exemption is available and any ambiguities herein shall be interpreted
accordingly; provided, however, that to the extent such an exemption is not available, the benefits provided under the Plan are intended to comply with the requirements of Section 409A to the extent necessary to avoid adverse personal
tax consequences and any ambiguities herein shall be interpreted accordingly. 
 Notwithstanding anything to the contrary
set forth herein, any payments and benefits provided under the Plan that constitute “deferred compensation” within the meaning of Section 409A shall not commence in connection with an Eligible Employee’s termination of employment
unless and until the Eligible Employee has also incurred a “separation from service,” as such term is defined in Treasury Regulations Section 1.409A-1(h) (“Separation from
Service”), unless the Company reasonably determines that such amounts may be provided to the Eligible Employee without causing the Eligible Employee to incur the adverse personal tax consequences under Section 409A. 

It is intended that (i) each installment of any benefits payable under the Plan to an Eligible Employee be regarded as a
separate “payment” for purposes of Treasury Regulations Section 1.409A-2(b)(2)(i), (ii) all payments of any such benefits under the Plan satisfy, to the greatest extent possible, the exemptions
from the application of Section 409A provided under Treasury Regulations Sections 1.409A-1(b)(4), 1.409A-1(b)(5) and
1.409A-1(b)(9)(iii), and (iii) any such benefits consisting of COBRA premiums also satisfy, to the greatest extent possible, the exemption from the application of Section 409A provided under Treasury
Regulations Section 1.409A-1(b)(9)(v). However, if the Company determines that any severance benefits payable under the Plan constitute “deferred compensation” under Section 409A and the
Eligible Employee is a “specified employee” of the Company, as such term is defined in Section 409A(a)(2)(B)(i), 

  
 7. 

 
then, solely to the extent necessary to avoid the imposition of the adverse personal tax consequences under Section 409A, (A) the timing of such severance benefit payments shall be
delayed until the earlier of (1) the date that is six months and one day after the Eligible Employee’s Separation from Service and (2) the date of the Eligible Employee’s death (such applicable date, the “Delayed
Initial Payment Date”), and (B) the Company shall (1) pay the Eligible Employee a lump sum amount equal to the sum of the severance benefit payments that the Eligible Employee would otherwise have received through the Delayed
Initial Payment Date if the commencement of the payment of the severance benefits had not been delayed pursuant to this paragraph and (2) commence paying the balance, if any, of the severance benefits in accordance with the applicable payment
schedule. 
 In no event shall payment of any severance benefits under the Plan be made prior to an Eligible Employee’s
termination date or prior to the effective date of the Release. If the Company determines that any severance payments or benefits provided under the Plan constitute “deferred compensation” under Section 409A, and the Eligible
Employee’s Separation from Service occurs at a time during the calendar year when the Release could become effective in the calendar year following the calendar year in which the Eligible Employee’s Separation from Service occurs, then
regardless of when the Release is returned to the Company and becomes effective, the Release will not be deemed effective, solely for purposes of the timing of payment of severance benefits under this Plan, any earlier than the latest permitted
effective date (the “Release Deadline”). If the Company determines that any severance payments or benefits provided under the Plan constitute “deferred compensation” under Section 409A, then except to the
extent that severance payments may be delayed until the Delayed Initial Payment Date pursuant to the preceding paragraph, on the first regular payroll date following the effective date of an Eligible Employee’s Release, the Company shall
(1) pay the Eligible Employee a lump sum amount equal to the sum of the severance benefit payments that the Eligible Employee would otherwise have received through such payroll date but for the delay in payment related to the effectiveness of
the Release and (2) commence paying the balance, if any, of the severance benefits in accordance with the applicable payment schedule. 

All payments under the Plan shall be subject to applicable withholding for federal, state and local taxes. 

Section 6.    TRANSFER AND ASSIGNMENT. 

The rights and obligations of an Eligible Employee under this Plan may not be transferred or assigned without the prior written
consent of the Company. This Plan shall be binding upon any entity or person who is a successor by merger, acquisition, consolidation or otherwise to the business formerly carried on by the Company without regard to whether or not such entity or
person actively assumes the obligations hereunder and without regard to whether or not a Change in Control occurs. 

Section 7.    RIGHT TO INTERPRET AND ADMINISTER
PLAN; AMENDMENT AND TERMINATION. 

(a)    Interpretation and Administration. Prior to the Closing, the Committee shall be the
Plan Administrator and shall have the exclusive discretion and authority to establish rules, forms, and procedures for the administration of the Plan and to construe and interpret the 

  
 8. 

 
Plan and to decide any and all questions of fact, interpretation, definition, computation or administration arising in connection with the operation of the Plan, including, but not limited to,
the eligibility to participate in the Plan and amount of benefits paid under the Plan. The rules, interpretations, computations and other actions of the Committee shall be binding and conclusive on all persons. Upon and after the Closing, the Plan
will be interpreted and administered in good faith by the Representative who shall be the Plan Administrator during such period. All actions taken by the Representative in interpreting the terms of the Plan and administering the Plan upon and after
the Closing will be final and binding on all Eligible Employees. Any references in this Plan to the “Committee” or “Plan Administrator” with respect to periods following the Closing shall mean the Representative. 

(b)    Amendment. The Plan Administrator reserves the right to amend this Plan at any time;
provided, however, that any amendment of the Plan will not be effective as to a particular employee who is or may be adversely impacted by such amendment or termination and has an effective Participation Agreement without the written consent
of such employee. 
 (c)    Termination. Unless otherwise extended by the Committee, the
Plan will automatically terminate following satisfaction of all the Company’s obligations under the Plan. 

Section 8.    NO IMPLIED EMPLOYMENT CONTRACT. 

The Plan shall not be deemed (i) to give any employee or other person any right to be retained in the employ of the
Company or (ii) to interfere with the right of the Company to discharge any employee or other person at any time, with or without cause, which right is hereby reserved. This Plan does not modify the
at-will employment status of any Eligible Employee. 

Section 9.    LEGAL CONSTRUCTION. 

This Plan is intended to be governed by and shall be construed in accordance with the Employee Retirement Income Security Act
of 1974 (“ERISA”) and, to the extent not preempted by ERISA, the laws of the State of California. 

Section 10.    CLAIMS, INQUIRIES AND APPEALS. 

(a)    Applications for Benefits and Inquiries. Any application for benefits, inquiries about
the Plan or inquiries about present or future rights under the Plan must be submitted to the Plan Administrator in writing by an applicant (or his or her authorized representative). The Plan Administrator is: 

Metacrine, Inc. 
 Compensation
Committee of the Board of Directors or Representative 
 Attention to: Chief Financial Officer 

3985 Sorrento Valley Blvd., Suite C 

San Diego, California 92121 

(b)    Denial of Claims. In the event that any application for benefits is denied in whole
or in part, the Plan Administrator must provide the applicant with written or electronic notice of the denial of the application, and of the applicant’s right to review the denial. Any 

  
 9. 

 
electronic notice will comply with the regulations of the U.S. Department of Labor. The notice of denial will be set forth in a manner designed to be understood by the applicant and will include
the following: 
 (1)    the specific reason or reasons for the denial; 

(2)    references to the specific Plan provisions upon which the denial is based; 

(3)    a description of any additional information or material that the Plan Administrator needs
to complete the review and an explanation of why such information or material is necessary; and 

(4)    an explanation of the Plan’s review procedures and the time limits applicable to such
procedures, including a statement of the applicant’s right to bring a civil action under Section 502(a) of ERISA following a denial on review of the claim, as described in Section 10(d) below. 

This notice of denial will be given to the applicant within 90 days after the Plan Administrator receives the application,
unless special circumstances require an extension of time, in which case, the Plan Administrator has up to an additional 90 days for processing the application. If an extension of time for processing is required, written notice of the extension will
be furnished to the applicant before the end of the initial 90 day period. 
 This notice of extension will describe the
special circumstances necessitating the additional time and the date by which the Plan Administrator is to render its decision on the application. 

(c)    Request for a Review. Any person (or that person’s authorized representative)
for whom an application for benefits is denied, in whole or in part, may appeal the denial by submitting a request for a review to the Plan Administrator within 60 days after the application is denied. A request for a review shall be in writing and
shall be addressed to: 
 Metacrine, Inc. 

Compensation Committee of the Board of Directors or Representative 

Attention to: Chief Financial Officer 

3985 Sorrento Valley Blvd., Suite C 

San Diego, California 92121 
 A
request for review must set forth all of the grounds on which it is based, all facts in support of the request and any other matters that the applicant feels are pertinent. The applicant (or his or her representative) shall have the opportunity to
submit (or the Plan Administrator may require the applicant to submit) written comments, documents, records, and other information relating to his or her claim. The applicant (or his or her representative) shall be provided, upon request and free of
charge, reasonable access to, and copies of, all documents, records and other information relevant to his or her claim. The review shall take into account all comments, documents, records and other information submitted by the applicant (or his or
her representative) relating to the claim, 

  
 10. 

 
without regard to whether such information was submitted or considered in the initial benefit determination. 

(d)    Decision on Review. The Plan Administrator will act on each request for review within
60 days after receipt of the request, unless special circumstances require an extension of time (not to exceed an additional 60 days), for processing the request for a review. If an extension for review is required, written notice of the extension
will be furnished to the applicant within the initial 60 day period. This notice of extension will describe the special circumstances necessitating the additional time and the date by which the Plan Administrator is to render its decision on the
review. The Plan Administrator will give prompt, written or electronic notice of its decision to the applicant. Any electronic notice will comply with the regulations of the U.S. Department of Labor. In the event that the Plan Administrator confirms
the denial of the application for benefits in whole or in part, the notice will set forth, in a manner calculated to be understood by the applicant, the following: 

(1)    the specific reason or reasons for the denial; 

(2)    references to the specific Plan provisions upon which the denial is based; 

(3)    a statement that the applicant is entitled to receive, upon request and free of charge,
reasonable access to, and copies of, all documents, records and other information relevant to his or her claim; and 

(4)    a statement of the applicant’s right to bring a civil action under Section 502(a)
of ERISA. 
 (e)    Rules and Procedures. The Plan Administrator will establish rules and
procedures, consistent with the Plan and with ERISA, as necessary and appropriate in carrying out its responsibilities in reviewing benefit claims. The Plan Administrator may require an applicant who wishes to submit additional information in
connection with an appeal from the denial of benefits to do so at the applicant’s own expense. 

(f)    Exhaustion of Remedies. No legal action for benefits under the Plan may be brought
until the applicant (i) has submitted a written application for benefits in accordance with the procedures described by Section 10(a) above, (ii) has been notified by the Plan Administrator that the application is denied,
(iii) has filed a written request for a review of the application in accordance with the appeal procedure described in Section 10(c) above, and (iv) has been notified that the Plan Administrator has denied the appeal. Notwithstanding
the foregoing, if the Plan Administrator does not respond to an Eligible Employee’s claim or appeal within the relevant time limits specified in this Section 10, the Eligible Employee may bring legal action for benefits under the Plan
pursuant to Section 502(a) of ERISA. 
 Section 11.    BASIS OF PAYMENTS
TO AND FROM PLAN. 
 The Plan shall be unfunded, and all cash
payments under the Plan shall be paid only from the general assets of the Company. 

  
 11. 

 Section 12.    OTHER PLAN INFORMATION.

 (a)    Employer and Plan Identification Numbers. The Employer Identification Number
assigned to the Company (which is the “Plan Sponsor” as that term is used in ERISA) by the Internal Revenue Service is 47-2297384. The Plan Number assigned to the Plan by the Plan Sponsor pursuant to the instructions of the Internal
Revenue Service is 502. 
 (b)    Ending Date for Plan’s Fiscal Year.
The date of the end of the fiscal year for the purpose of maintaining the Plan’s records is December 31. 

(c)    Agent for the Service of Legal Process. The agent for the service of legal process
with respect to the Plan is: 
 Metacrine, Inc. 

Attention to: Chief Financial Officer 

3985 Sorrento Valley Blvd., Suite C 

San Diego, California 92121 
 In
addition, service of legal process may be made upon the Plan Administrator. 
 (d)    Plan
Sponsor. The “Plan Sponsor” is: 
 Metacrine, Inc. 

3985 Sorrento Valley Blvd., Suite C 

San Diego, California 92121 
 (858)369-7800 
 (e)    Plan Administrator. The Plan
Administrator is the Committee prior to the Closing and the Representative upon and following the Closing. The Plan Administrator’s contact information is: 

Metacrine, Inc. 
 Compensation
Committee of the Board of Directors or Representative 
 3985 Sorrento Valley Blvd., Suite C 

San Diego, California 92121 
 The
Plan Administrator is the named fiduciary charged with the responsibility for administering the Plan. 

Section 13.    STATEMENT OF ERISA RIGHTS. 

Participants in this Plan (which is a welfare benefit plan sponsored by Metacrine, Inc.) are entitled to certain rights and
protections under ERISA. If you are an Eligible Employee, you are considered a participant in the Plan and, under ERISA, you are entitled to: 

(a)    Receive Information About Your Plan and Benefits 

  
 12. 

 (1)    Examine, without charge, at the Plan
Administrator’s office and at other specified locations, such as worksites, all documents governing the Plan and a copy of the latest annual report (Form 5500 Series), if applicable, filed by the Plan with the U.S. Department of Labor and
available at the Public Disclosure Room of the Employee Benefits Security Administration; 

(2)    Obtain, upon written request to the Plan Administrator, copies of documents governing the
operation of the Plan and copies of the latest annual report (Form 5500 Series), if applicable, and an updated (as necessary) Summary Plan Description. The Administrator may make a reasonable charge for the copies; and 

(3)    Receive a summary of the Plan’s annual financial report, if applicable. The Plan
Administrator is required by law to furnish each Eligible Employee with a copy of this summary annual report. 

(b)    Prudent Actions by Plan Fiduciaries. In addition to creating rights for Plan Eligible
Employees, ERISA imposes duties upon the people who are responsible for the operation of the employee benefit plan. The people who operate the Plan, called “fiduciaries” of the Plan, have a duty to do so prudently and in the interest of
you and other Eligible Employees and beneficiaries. No one, including your employer, your union or any other person, may fire you or otherwise discriminate against you in any way to prevent you from obtaining a Plan benefit or exercising your rights
under ERISA. 
 (c)    Enforce Your Rights. If your claim for a Plan benefit is denied or
ignored, in whole or in part, you have a right to know why this was done, to obtain copies of documents relating to the decision without charge, and to appeal any denial, all within certain time schedules. 

Under ERISA, there are steps you can take to enforce the above rights. For instance, if you request a copy of Plan documents
or the latest annual report from the Plan, if applicable, and do not receive them within 30 days, you may file suit in a Federal court. In such a case, the court may require the Plan Administrator to provide the materials and pay you up to $110 a
day until you receive the materials, unless the materials were not sent because of reasons beyond the control of the Plan Administrator. 

If you have a claim for benefits which is denied or ignored, in whole or in part, you may file suit in a state or Federal
court. 
 If you are discriminated against for asserting your rights, you may seek assistance from the U.S. Department of
Labor, or you may file suit in a Federal court. The court will decide who should pay court costs and legal fees. If you are successful, the court may order the person you have sued to pay these costs and fees. If you lose, the court may order you to
pay these costs and fees, for example, if it finds your claim is frivolous. 

(d)    Assistance with Your Questions. If you have any questions about the Plan, you should
contact the Plan Administrator. If you have any questions about this statement or about your rights under ERISA, or if you need assistance in obtaining documents from the Plan Administrator, you should contact the nearest office of the Employee
Benefits Security Administration, U.S. Department of Labor, listed in your telephone directory or the Division of 

  
 13. 

 
Technical Assistance and Inquiries, Employee Benefits Security Administration, U.S. Department of Labor, 200 Constitution Avenue N.W., Washington, D.C. 20210. You may also obtain certain
publications about your rights and responsibilities under ERISA by calling the publications hotline of the Employee Benefits Security Administration. 

  
 14. 

 APPENDIX A 

PARTICIPATION AGREEMENT 
  

 METACRINE, INC. 

SEVERANCE BENEFIT PLAN 

PARTICIPATION AGREEMENT 

Name:
                                         
    
 Section 1.    ELIGIBILITY. 

You have been designated as eligible to participate in the Metacrine, Inc. Severance Benefit Plan (the
“Plan”), a copy of which is attached as EXHIBIT A to this Participation Agreement (the “Agreement”). Capitalized terms not explicitly
defined in this Agreement but defined in the Plan shall have the same definitions as in the Plan. You will receive the benefits set forth below if you meet all the eligibility requirements set forth in the Plan, including, without limitation,
executing the required Release within the applicable time period set forth therein and provided that such Release becomes effective in accordance with its terms. Notwithstanding the schedule for provision of benefits as set forth below, the schedule
and timing of payment of any benefits under this Agreement is subject to any delay in payment that may be required under Section 5 of the Plan. 

Section 2.    CHANGE IN CONTROL SEVERANCE BENEFITS.

 If you are terminated in a Covered Termination that occurs during the Change in Control Period, you will receive the
severance benefits set forth in this Section 2. All severance benefits described herein are subject to standard deductions and withholdings. 

(a)    Base Salary. You shall receive a cash payment equal to your Base Salary (ignoring any
decrease that forms the basis for your resignation for Good Reason, if applicable), for [______]1 months following the date of termination (the “Severance Period”). Upon
and following the IPO Date the Severance Period shall be [______]2 months following the date of termination. The Base Salary payment will be paid to you in a lump sum cash payment no later than
the second payroll cycle following the later of (i) the effective date of the Release or (ii) the Closing, but in any event not later than March 15 of the year following the year in which the Covered Termination occurs. 

(b)    Bonus Payment. You will be entitled to the annual target cash bonus established for
you, if any, pursuant to the annual performance bonus or annual variable compensation plan established by the Board of Directors or Committee (or any authorized committee or designee thereof) for the year in which the Covered Termination occurs. If
at the time of the Covered Termination you are eligible for the annual target cash bonus for the year in which the Covered Termination occurs, but the target percentage (or target dollar amount, if specified as such in the applicable bonus plan) for
such bonus has not yet been established for such year, the target percentage shall be the target percentage established for you for the preceding year (but adjusted, if necessary for your position for the year in which the Covered Termination
occurs). 
  
  

	1 	 12 months for CEO, 9 months for C-Level Executives, and 6 months for
VPs 

	2 	 18 months for CEO, 12 months for C-Level Executives, and 9 months for
VPs 

 
For the avoidance of doubt, the amount of the annual target bonus to which you are entitled under this Section 2(b) will be calculated (1) assuming all articulated performance goals for
such bonus (including, but not limited to, corporate and individual performance, if applicable), for the year of the Covered Termination was achieved at target levels; (2) as if you had provided services for the entire year for which the bonus
relates; and (3) ignoring any reduction in your Base Salary that would give rise to your right to resignation for Good Reason (such bonus to which you are entitled under this Section 2(b), the “Annual Target Bonus Severance
Payment”). The Annual Target Bonus Severance Payment shall be paid in a lump sum cash payment no later than the second payroll cycle following the later of (i) the effective date of the Release or (ii) the Closing, but in any
event not later than March 15 of the year following the year in which the Covered Termination occurs. 

(c)    Payment of Continued Group Health Plan Benefits. If you timely elect continued group
health plan continuation coverage under the Consolidated Omnibus Budget Reconciliation Act of 1985 (“COBRA”) following your Covered Termination date, the Company shall pay directly to the carrier the full amount of your COBRA
premiums on behalf of you for your continued coverage under the Company’s group health plans, including coverage for your eligible dependents, until the earliest of (i) the end of the Severance Period following the date of your Covered
Termination, (ii) the expiration of your eligibility for the continuation coverage under COBRA, or (iii) the date when you become eligible for substantially equivalent health insurance coverage in connection with new employment (such
period from your termination date through the earliest of (i) through (iii), the “COBRA Payment Period”). Upon the conclusion of such period of insurance premium payments made by the Company, you will be responsible for
the entire payment of premiums (or payment for the cost of coverage) required under COBRA for the duration of your eligible COBRA coverage period, if any. For purposes of this Section, (1) references to COBRA shall be deemed to refer also to
analogous provisions of state law and (2) any applicable insurance premiums that are paid by the Company shall not include any amounts payable by you under an Internal Revenue Code Section 125 health care reimbursement plan, which amounts,
if any, are your sole responsibility. 
 Notwithstanding the foregoing, if at any time the Company determines, in its sole
discretion, that it cannot provide the COBRA premium benefits without potentially incurring financial costs or penalties under applicable law (including, without limitation, Section 2716 of the Public Health Service Act), then in lieu of paying
COBRA premiums directly to the carrier on your behalf, the Company will instead pay you on the last day of each remaining month of the COBRA Payment Period a fully taxable cash payment equal to the value of your monthly COBRA premium for the first
month of COBRA coverage, subject to applicable tax withholding (such amount, the “Special Severance Payment”), such Special Severance Payment to be made without regard to your election of COBRA coverage or payment of COBRA
premiums and without regard to your continued eligibility for COBRA coverage during the COBRA Payment Period. Such Special Severance Payment shall end upon expiration of the COBRA Payment Period. 

(d)    Equity Acceleration. The vesting and exercisability of each outstanding unvested
stock option and other stock award, as applicable, that you hold covering Company common stock (each, an “Equity Award”) shall be accelerated in full and any reacquisition or repurchase rights held by the Company in respect
of common stock issued pursuant to any Equity Award granted to you shall lapse in full. For purposes of determining the number of shares that 

 
will vest pursuant to the foregoing provision with respect to any performance based vesting Equity Award for which the performance period has not ended and that has multiple vesting levels
depending upon the level of performance, vesting acceleration with respect to any ongoing performance period(s) shall occur with respect to the number of shares subject to the award as if the applicable performance criteria had been attained at a
100% level or, if greater, based on actual performance as of your Covered Termination. If necessary to give effect to this Section 2(d), if your Covered Termination occurs prior to a Change in Control, all of the Equity Awards you hold as of
immediately prior to your Covered Termination shall remain outstanding after your Covered Termination for at least until the earlier of (i) 3 months after your Covered Termination or (ii) the Closing, if sooner. Notwithstanding anything to the
contrary set forth herein, your Equity Awards shall remain subject to the terms of the applicable Company plan and award documents under which such Equity Award was granted, including any provision for earlier termination of such Equity Awards. 

Section 3.    
NON-CHANGE IN CONTROL SEVERANCE BENEFITS. 

Upon and following the IPO Date, if you are terminated in a Covered Termination that occurs at a time that is not during the
Change in Control Period, you will receive the cash payment described in Section 2(a) above and the COBRA benefits described in Section 2(c) above, but the Severance Period for purposes of calculating such benefits shall be [______]3 months following the date of termination. You shall not be eligible to receive any other benefits under the Plan except a described in Section 2(a) and Section 2(c) above. All severance
benefits described herein are subject to standard deductions and withholdings. 
 For the avoidance of doubt, in no event shall you be
entitled to benefits under both Section 2 and this Section 3. If you are eligible for severance benefits under both Section 2 and this Section 3, you shall receive the benefits set forth in Section 2 and such benefits shall
be reduced by any benefits previously provided to you under Section 3. 
 Section 4.    ACKNOWLEDGEMENTS.

 As a condition to participation in the Plan, you hereby acknowledge each of the following: 

(a)    The benefits that may be provided to you under this Agreement are subject to certain
reductions and termination under Section 2 and Section 3 of the Plan. 
 (b)    Your
eligibility for and receipt of any severance benefits to which you may become entitled as described in Section 2 or Section 3 above is expressly contingent upon your compliance with the terms and conditions of the Release and the terms and
conditions of your [Proprietary Information, Inventions, and Non-Solicitation Agreement] (or similar agreement) with the Company, as may be amended from time to time (the “Proprietary
Agreement”). Severance benefits under this Agreement shall immediately cease in the event of your violation of the provisions of the Release or the Proprietary Agreement. 

(c)    Except as set forth in Section 2 of the Plan with respect to an Individual Agreement to
the extent such Individual Agreement provides more advantageous benefits to you, 
  

 

	3 	 12 months for CEO, 9 months for C-Level Executives, and 6 months for
VPs 

 
this Agreement and the Plan supersede and replace any change in control or severance benefits under any Individual Agreement. 

To accept the terms of this Agreement and participate in the Plan, please sign and date this Agreement in the space provided below and return
it to _____________________ no later than _________, 20184. 
  

			
	Metacrine, Inc.
		
	By:	 	 
	
	 Ken Song, M.D.

Chief Executive Officer

	
	Eligible Employee
	
	 
	 [Insert Name]

		
	 Date:
	 	 

  

	4 	 Note to draft: This date should be 30 days after the Participation Agreement is delivered to the employee.

 EXHIBIT A 

SEVERANCE BENEFIT PLAN

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