Document:

EX-4.1

 Exhibit 4.1 

SYNDAX PHARMACEUTICALS, INC. 

WARRANT TO PURCHASE COMMON STOCK 
  

			
		  	 Number of Shares:
[                ]
 (subject to adjustment)

	Warrant No. [    ]	  	Original Issue Date: February 4, 2020

 Syndax Pharmaceuticals, Inc., a Delaware corporation (the “Company”), hereby certifies that,
for good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, [     ]. or its permitted registered assigns (the “Holder”), is entitled, subject to the terms set forth below,
to purchase from the Company up to a total of [             ] shares of common stock, $0.0001 par value per share (the “Common Stock”), of the Company (each such share, a
“Warrant Share” and all such shares, the “Warrant Shares”) at an exercise price per share equal to $0.0001 per share (as adjusted from time to time as provided in Section 9 herein, the
“Exercise Price”), upon surrender of this Warrant to Purchase Common Stock (including any Warrants to Purchase Common Stock issued in exchange, transfer or replacement hereof, the “Warrant”) at any time and from
time to time on or after the date hereof (the “Original Issue Date”) and through and including 5:30 P.M., New York City time, on the date upon which this Warrant is fully exercised (the “Expiration Date”), and
subject to the following terms and conditions: 
 1. Definitions. For purposes of this Warrant, the following terms shall have the following
meanings: 
 (a) “Affiliate” means any Person directly or indirectly controlled by, controlling or under common control
with, a Holder, but only for so long as such control shall continue. For purposes of this definition, “control” (including, with correlative meanings, “controlled by,” “controlling” and “under common control
with”) means, with respect to a Person, possession, direct or indirect, of (a) the power to direct or cause direction of the management and policies of such Person (whether through ownership of securities or partnership or other ownership
interests, by contract or otherwise), or (b) at least 50% of the voting securities (whether directly or pursuant to any option, warrant or other similar arrangement) or other comparable equity interests. 

(b) “Commission” means the United States Securities and Exchange Commission. 

(c) “Closing Sale Price” means, for any security as of any date, the last trade price for such security on the Principal
Trading Market for such security, as reported by Bloomberg Financial Markets, or, if such Principal Trading Market begins to operate on an extended hours basis and does not designate the last trade price, then the last trade price of such security
prior to 4:00 P.M., New York City time, as reported by Bloomberg Financial Markets, or if the foregoing do not apply, the last trade price of such security in the
over-the-counter market on the electronic bulletin board for such security as reported by Bloomberg Financial Markets, or, if no last trade price is reported for such
security by Bloomberg Financial Markets, the average of the bid and ask prices, of any market makers for such security as reported in the “pink sheets” by Pink Sheets LLC. If the Closing Sale Price cannot be calculated for a security on a
particular date on any of the foregoing bases, the Closing Sale Price of such security on such date shall be the fair market value as mutually determined by the Company and the Holder. If the Company and the Holder are unable to agree upon the fair
market value of such security, then the Board of Directors of the Company shall use its good faith judgment to determine the fair market value. The Board of Directors’ determination shall be binding upon all parties absent demonstrable error.
All such determinations shall be appropriately adjusted for any stock dividend, stock split, stock combination or other similar transaction during the applicable calculation period. 

(d) “Principal Trading Market” means the national securities exchange or other trading market on which the Common Stock is
primarily listed on and quoted for trading, which, as of the Original Issue Date, shall be The Nasdaq Global Select Market. 
 (e)
“Securities Act” means the Securities Act of 1933, as amended. 
 (f) “Trading Day” means any weekday on
which the Principal Trading Market is open for trading. 
 (g) “Transfer Agent” means Computershare Trust Company, N.A.,
the Company’s transfer agent and registrar for the Common Stock, and any successor appointed in such capacity. 

  
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 2. Registration of Warrants. The Company shall register this Warrant, upon records to be maintained
by the Company for that purpose (the “Warrant Register”), in the name of the record Holder (which shall include the initial Holder or, as the case may be, any registered assignee to which this Warrant is permissibly assigned
hereunder) from time to time. The Company may deem and treat the registered Holder of this Warrant as the absolute owner hereof for the purpose of any exercise hereof or any distribution to the Holder, and for all other purposes, absent actual
notice to the contrary. 
 3. Registration of Transfers. Subject to compliance with all applicable securities laws, the Company shall, or will cause
its Transfer Agent to, register the transfer of all or any portion of this Warrant in the Warrant Register, upon surrender of this Warrant, and payment for all applicable transfer taxes (if any). Upon any such registration or transfer, a new warrant
to purchase Common Stock in substantially the form of this Warrant (any such new warrant, a “New Warrant”) evidencing the portion of this Warrant so transferred shall be issued to the transferee, and a New Warrant evidencing the
remaining portion of this Warrant not so transferred, if any, shall be issued to the transferring Holder. The acceptance of the New Warrant by the transferee thereof shall be deemed the acceptance by such transferee of all of the rights and
obligations in respect of the New Warrant that the Holder has in respect of this Warrant. The Company shall, or will cause its Transfer Agent to, prepare, issue and deliver at the Company’s own expense any New Warrant under this
Section 3. Until due presentment for registration of transfer, the Company may treat the registered Holder hereof as the owner and holder for all purposes, and the Company shall not be affected by any notice to the
contrary. 
 4. Exercise and Duration of Warrants. 

(a) All or any part of this Warrant shall be exercisable by the registered Holder in any manner permitted by
Section 10 of this Warrant at any time and from time to time on or after the Original Issue Date and through and including 5:30 P.M. New York City time, on the Expiration Date. At 5:30 P.M., New York City time, on the
Expiration Date, the portion of this Warrant not exercised prior thereto shall be and become void and of no value and this Warrant shall be terminated and no longer outstanding. 

(b) The Holder may exercise this Warrant by delivering to the Company (i) an exercise notice, in the form attached as Schedule 1
hereto (the “Exercise Notice”), completed and duly signed, and (ii) payment of the Exercise Price for the number of Warrant Shares as to which this Warrant is being exercised (which may take the form of a “cashless
exercise” if so indicated in the Exercise Notice pursuant to Section 10 below), and the date on which the last of such items is delivered to the Company (as determined in accordance with the notice provisions hereof)
is an “Exercise Date.” The Holder shall not be required to deliver the original Warrant in order to effect an exercise hereunder. Execution and delivery of the Exercise Notice shall have the same effect as cancellation of the
original Warrant and issuance of a New Warrant evidencing the right to purchase the remaining number of Warrant Shares. 
 5. Delivery of Warrant
Shares. 
 (a) Upon exercise of this Warrant, the Company shall promptly (but in no event later than two Trading Days after the Exercise
Date), upon the request of the Holder, credit such aggregate number of shares of Common Stock to which the Holder is entitled pursuant to such exercise to the Holder’s or its designee’s balance account with The Depository Trust Company
(“DTC”) through its Deposit Withdrawal Agent Commission system, or if the Transfer Agent is not participating in the Fast Automated Securities Transfer Program (the “FAST Program”) or if the certificates are
required to bear a legend regarding restriction on transferability, issue and dispatch by overnight courier to the address as specified in the Exercise Notice, a certificate, registered in the Company’s share register in the name of the Holder
or its designee, for the number of shares of Common Stock to which the Holder is entitled pursuant to such exercise. The Holder, or any natural person or legal entity (each, a “Person”) permissibly so designated by the Holder to
receive Warrant Shares, shall be deemed to have become the holder of record of such Warrant Shares as of the Exercise Date, irrespective of the date such Warrant Shares are credited to the Holder’s DTC account or the date of delivery of the
certificates evidencing such Warrant Shares, as the case may be. 
 (b) If by the close of the second Trading Day after the Exercise Date,
the Company fails to deliver to the Holder a certificate representing the required number of Warrant Shares in the manner required pursuant to Section 5(a) or fails to credit the Holder’s balance account with DTC for
such number of Warrant Shares to which the Holder is entitled, and if after such second Trading Day and prior to the receipt of such Warrant Shares, the Holder purchases (in an open market transaction or otherwise) shares of Common Stock to deliver
in satisfaction of a sale by the Holder of the Warrant Shares which the Holder anticipated receiving upon such exercise (a “Buy-In”), then the Company shall, within two Trading Days after the
Holder’s request and in the Holder’s sole discretion, either (1) pay in cash to the Holder an amount equal to the Holder’s total purchase price (including brokerage commissions, if any) for the shares of Common Stock so purchased
(the “Buy-In Price”), at which point the Company’s obligation to deliver such certificate (and to issue such Warrant Shares) shall terminate or (2) promptly honor its obligation to
deliver to the Holder a certificate or certificates representing such Warrant 

  
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Shares and pay cash to the Holder in an amount equal to the excess (if any) of Holder’s total purchase price (including brokerage commissions, if any) for the shares of Common Stock so
purchased in the Buy-In over the product of (A) the number of shares of Common Stock purchased in the Buy-In, times (B) the Closing Sale Price of a share of
Common Stock on the Exercise Date. 
 (c) To the extent permitted by law and subject to 5(b), the Company’s obligations to issue and
deliver Warrant Shares in accordance with and subject to the terms hereof (including the limitations set forth in Section 11 below) are absolute and unconditional, irrespective of any action or inaction by the Holder to
enforce the same, any waiver or consent with respect to any provision hereof, the recovery of any judgment against any Person or any action to enforce the same, or any setoff, counterclaim, recoupment, limitation or termination, or any breach or
alleged breach by the Holder or any other Person of any obligation to the Company or any violation or alleged violation of law by the Holder or any other Person, and irrespective of any other circumstance that might otherwise limit such obligation
of the Company to the Holder in connection with the issuance of Warrant Shares. Subject to Section 5(b), nothing herein shall limit the Holder’s right to pursue any other remedies available to it hereunder, at law or in equity including,
without limitation, a decree of specific performance and/or injunctive relief with respect to the Company’s failure to timely deliver certificates representing shares of Common Stock upon exercise of the Warrant as required pursuant to the
terms hereof. 
 6. Charges, Taxes and Expenses. Issuance and delivery of certificates for shares of Common Stock upon exercise of this Warrant shall
be made without charge to the Holder for any issue or transfer tax, transfer agent fee or other incidental tax or expense (excluding any applicable stamp duties) in respect of the issuance of such certificates, all of which taxes and expenses shall
be paid by the Company; provided, however, that the Company shall not be required to pay any tax that may be payable in respect of any transfer involved in the registration of any certificates for Warrant Shares or the Warrants in a name
other than that of the Holder or an Affiliate thereof. The Holder shall be responsible for all other tax liability that may arise as a result of holding or transferring this Warrant or receiving Warrant Shares upon exercise hereof. 

7. Replacement of Warrant. If this Warrant is mutilated, lost, stolen or destroyed, the Company shall issue or cause to be issued in exchange and
substitution for and upon cancellation hereof, or in lieu of and substitution for this Warrant, a New Warrant, but only upon receipt of evidence reasonably satisfactory to the Company of such loss, theft or destruction (in such case) and, in each
case, a customary and reasonable indemnity and surety bond, if requested by the Company. Applicants for a New Warrant under such circumstances shall also comply with such other reasonable regulations and procedures and pay such other reasonable
third-party costs as the Company may prescribe. If a New Warrant is requested as a result of a mutilation of this Warrant, then the Holder shall deliver such mutilated Warrant to the Company as a condition precedent to the Company’s obligation
to issue the New Warrant. 
 8. Reservation of Warrant Shares. The Company covenants that it will at all times while this Warrant is outstanding
reserve and keep available out of the aggregate of its authorized but unissued and otherwise unreserved Common Stock, solely for the purpose of enabling it to issue Warrant Shares upon exercise of this Warrant as herein provided, the number of
Warrant Shares that are initially issuable and deliverable upon the exercise of this entire Warrant, free from preemptive rights or any other contingent purchase rights of persons other than the Holder (taking into account the adjustments and
restrictions of Section 9). The Company covenants that all Warrant Shares so issuable and deliverable shall, upon issuance and the payment of the applicable Exercise Price in accordance with the terms hereof, be duly and
validly authorized, issued and fully paid and nonassessable. The Company will take all such action as may be reasonably necessary to assure that such shares of Common Stock may be issued as provided herein without violation of any applicable law or
regulation, or of any requirements of any securities exchange or automated quotation system upon which the Common Stock may be listed. 
 9. Certain
Adjustments. The number of Warrant Shares issuable upon exercise of this Warrant is subject to adjustment from time to time as set forth in this Section 9. 

(a) Stock Dividends and Splits. If the Company, at any time while this Warrant is outstanding, (i) pays a stock dividend on its
Common Stock or otherwise makes a distribution on any class of capital stock issued and outstanding on the Original Issue Date and in accordance with the terms of such stock on the Original Issue Date or as amended, that is payable in shares of
Common Stock, (ii) subdivides its outstanding shares of Common Stock into a larger number of shares of Common Stock, (iii) combines its outstanding shares of Common Stock into a smaller number of shares of Common Stock or (iv) issues
by reclassification of shares of capital stock any additional shares of Common Stock of the Company, then in each such case the number of Warrant Shares then underlying this Warrant shall be divided by a fraction, the numerator of which shall be the
number of shares of Common Stock outstanding immediately before such event and the denominator of which shall be the number of shares of Common Stock outstanding immediately after such event. Any adjustment made pursuant to clause (i) of this
paragraph shall become effective immediately after the record date for the determination of stockholders entitled to receive such dividend or distribution, provided, however, that if such record date shall have been fixed and such dividend is

  
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not fully paid on the date fixed therefor, the number of Warrant Shares shall be recomputed accordingly as of the close of business on such record date and thereafter the Warrant Shares shall be
adjusted pursuant to this paragraph as of the time of actual payment of such dividends. Any adjustment pursuant to clause (ii) or (iii) of this paragraph shall become effective immediately after the effective date of such subdivision or
combination. 
 (b) Pro Rata Distributions. If the Company, at any time while this Warrant is outstanding, distributes to all holders
of Common Stock for no consideration (i) evidences of its indebtedness, (ii) any security (other than a distribution of Common Stock covered by the preceding paragraph), (iii) rights or warrants to subscribe for or purchase any security,
or (iv) cash or any other asset (in each case, “Distributed Property”), then, upon any exercise of this Warrant that occurs after the record date fixed for determination of stockholders entitled to receive such distribution,
the Holder shall be entitled to receive, in addition to the Warrant Shares otherwise issuable upon such exercise (if applicable), the Distributed Property that such Holder would have been entitled to receive in respect of such number of Warrant
Shares had the Holder been the record holder of such Warrant Shares immediately prior to such record date without regard to any limitation on exercise contained therein. 

(c) Fundamental Transactions. If, at any time while this Warrant is outstanding (i) the Company effects any merger or
consolidation of the Company with or into another Person, in which the Company is not the surviving entity or the stockholders of the Company immediately prior to such merger or consolidation do not own, directly or indirectly, at least 50% of the
voting power of the surviving entity immediately after such merger or consolidation, (ii) the Company effects any sale to another Person of all or substantially all of its assets in one transaction or a series of related transactions,
(iii) pursuant to any tender offer or exchange offer (whether by the Company or another Person), holders of capital stock who tender shares representing more than 50% of the voting power of the capital stock of the Company and the Company or
such other Person, as applicable, accepts such tender for payment, (iv) the Company consummates a stock purchase agreement or other business combination (including, without limitation, a reorganization, recapitalization, spin-off or scheme of arrangement) with another Person whereby such other Person acquires more than the 50% of the voting power of the capital stock of the Company (except for any such transaction in which the
stockholders of the Company immediately prior to such transaction maintain, in substantially the same proportions, the voting power of such Person immediately after the transaction) or (v) the Company effects any reclassification of the Common
Stock or any compulsory share exchange pursuant to which the Common Stock is effectively converted into or exchanged for other securities, cash or property (other than as a result of a subdivision or combination of shares of Common Stock covered by
Section 9(a) above) (in any such case, a “Fundamental Transaction”), then following such Fundamental Transaction the Holder shall have the right to receive, upon exercise of this Warrant, the same amount
and kind of securities, cash or property as it would have been entitled to receive upon the occurrence of such Fundamental Transaction if it had been, immediately prior to such Fundamental Transaction, the holder of the number of Warrant Shares then
issuable upon exercise in full of this Warrant without regard to any limitations on exercise contained herein (the “Alternate Consideration”). The Company shall not effect any Fundamental Transaction in which the Company is not the
surviving entity or the Alternate Consideration includes securities of another Person unless (i) the Alternate Consideration is solely cash and the Company provides for the simultaneous “cashless exercise” of this Warrant pursuant to
Section 10 below or (ii) prior to or simultaneously with the consummation thereof, any successor to the Company, surviving entity or other Person (including any purchaser of assets of the Company) shall assume the obligation to deliver to
the Holder, such Alternate Consideration as, in accordance with the foregoing provisions, the Holder may be entitled to receive, and the other obligations under this Warrant. The provisions of this paragraph (c) shall similarly apply to
subsequent transactions analogous of a Fundamental Transaction type. 
 (d) Calculations. All calculations under this
Section 9 shall be made to the nearest share. 
 (e) Notice of Adjustments. Upon the occurrence of each
adjustment pursuant to this Section 9, the Company at its expense will, at the written request of the Holder, promptly compute such adjustment, in good faith, in accordance with the terms of this Warrant and prepare a
certificate setting forth such adjustment, including a statement of the adjusted number or type of Warrant Shares or other securities issuable upon exercise of this Warrant (as applicable), describing the transactions giving rise to such adjustments
and showing in detail the facts upon which such adjustment is based. Upon written request, the Company will promptly deliver a copy of each such certificate to the Holder and to the Company’s transfer agent. 

(f) Notice of Corporate Events. If, while this Warrant is outstanding, the Company (i) declares a dividend or any other
distribution of cash, securities or other property in respect of its Common Stock, including, without limitation, any granting of rights or warrants to subscribe for or purchase any capital stock of the Company or any subsidiary,
(ii) authorizes or approves, enters into any agreement contemplating or solicits stockholder approval for any Fundamental Transaction or (iii) authorizes the voluntary dissolution, liquidation or winding up of the affairs of the Company,
then, except if such notice and the contents thereof shall be deemed to constitute material non-public information, the Company shall deliver to the Holder a notice of such transaction at least ten
(10) days prior to the applicable record or effective date on which a Person would need 

  
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to hold Common Stock in order to participate in or vote with respect to such transaction; provided, however, that the failure to deliver such notice or any defect therein shall not affect
the validity of the corporate action required to be described in such notice. In addition, if while this Warrant is outstanding, the Company authorizes or approves, enters into any agreement contemplating or solicits stockholder approval for any
Fundamental Transaction contemplated by Section 9(c), other than a Fundamental Transaction under clause (iii) of Section 9(c), the Company shall deliver to the Holder a notice of such Fundamental Transaction at
least thirty (30) days prior to the date such Fundamental Transaction is consummated. Holder agrees to maintain any information disclosed pursuant to this Section 9(f) in confidence until such information is publicly available, and shall
comply with applicable law with respect to trading in the Company’s securities following receipt any such information. 
 10. Payment of Exercise
Price. Notwithstanding anything contained herein to the contrary, the Holder may, in its sole discretion, satisfy its obligation to pay the Exercise Price through a “cashless exercise,” in which event the Company shall issue to the
Holder the number of Warrant Shares determined as follows: 
 X = Y [(A-B)/A] 

where: 
 “X” equals the
number of Warrant Shares to be issued to the Holder; 
 “Y” equals the total number of Warrant Shares with respect to which this
Warrant is then being exercised; 
 “A” equals the average of the Closing Sale Prices of the shares of Common Stock (as reported
by Bloomberg Financial Markets) for the five (5) consecutive Trading Days ending on the date immediately preceding the Exercise Date; and 

“B” equals the Exercise Price then in effect for the applicable Warrant Shares at the time of such exercise. 

For purposes of Rule 144 promulgated under the Securities Act, it is intended, understood and acknowledged that the Warrant Shares issued in a “cashless
exercise” transaction shall be deemed to have been acquired by the Holder, and the holding period for the Warrant Shares shall be deemed to have commenced, on the date this Warrant was originally issued (provided that the Commission continues
to take the position that such treatment is proper at the time of such exercise). Except as set forth in Section 5(b) (Buy-In remedy) and Section 12 (payment of cash in lieu of fractional shares), in
no event will the exercise of this Warrant be settled in cash. 
 11. Limitations on Exercise. 

(a) Notwithstanding anything to the contrary contained herein, the number of Warrant Shares that may be acquired by the Holder upon any
exercise of this Warrant (or otherwise in respect hereof) shall be limited to the extent necessary to ensure that, following such exercise (or other issuance), the total number of shares of Common Stock then beneficially owned by the Holder and its
Affiliates and any other Persons whose beneficial ownership of Common Stock would be aggregated with the Holder’s for purposes of Section 13(d) of the Exchange Act, does not exceed 9.99% of the total number of then issued and outstanding
shares of Common Stock (including for such purpose the shares of Common Stock issuable upon such exercise), it being acknowledged by the Holder that the Company is not representing to such Holder that such calculation is in compliance with
Section 13(d) of the Exchange Act and such Holder is solely responsible for any schedules required to be filed in accordance therewith. In addition, a determination under this Section 11(a) as to any group status shall
be determined in accordance with Section 13(d) of the Exchange Act and the rules and regulations promulgated thereunder. For purposes of this Section 11(a), in determining the number of outstanding shares of Common
Stock, the Holder may rely on the number of outstanding shares of Common Stock as reflected in (x) the Company’s most recent Form 10-Q or Form 10-K, as the
case may be, (y) a more recent public announcement by the Company or (z) any other notice by the Company or the Transfer Agent setting forth the number of shares of Common Stock outstanding. Upon the written request of the Holder, the
Company shall, within three (3) Trading Days, confirm orally and in writing to such Holder the number of shares of Common Stock then outstanding. By written notice to the Company, the Holder may waive the provisions of this
Section 11(a) or increase or decrease the beneficial ownership limitation to such percentage of the number of shares of the Common Stock outstanding immediately after giving effect to the issuance of shares of Common Stock
upon exercise of this Warrant as the Holder shall determine, in its sole discretion; provided that, any notice to increase the beneficial ownership limitation not be effective until the sixty-first
(61st) day after such notice is delivered to the Company, and subject to Section 11(b), and the provisions of this Section 11(a) shall continue
to apply. Upon such a change by a Holder of the beneficial ownership limitation from such 9.99% limitation to such other percentage limitation, the beneficial ownership limitation may not be 

  
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further waived or increased by such Holder without first providing the minimum notice required by this Section 11(a). Notwithstanding the foregoing, at any time
following notice of a Fundamental Transaction under Section 9(f)(ii) with respect to a Section 9(c)(iii) Fundamental Transaction, the Holder may waive and/or change the beneficial ownership
limitation effective immediately upon written notice to the Company and may reinstitute a beneficial ownership limitation at any time thereafter effective immediately upon written notice to the Company. 

(b) Notwithstanding anything to the contrary contained herein, including Section 11(a), the Company shall not effect
any exercise of this Warrant, and the Holder shall not be entitled to exercise this Warrant for a number of Warrant Shares in excess of that number of Warrant Shares which, upon giving effect to such exercise, would cause (i) the aggregate
number of shares of Common Stock beneficially owned by the Holder and its Affiliates and any other Persons whose beneficial ownership of Common Stock would be aggregated with the Holder’s for purposes of Section 13(d) of the Exchange Act,
to exceed 19.99% of the total number of issued and outstanding shares of Common Stock of the Company following such exercise, or (ii) the combined voting power of the securities of the Company beneficially owned by the Holder and its Affiliates
and any other Persons whose beneficial ownership of Common Stock would be aggregated with the Holder’s for purposes of Section 13(d) of the Exchange Act to exceed 19.99% of the combined voting power of all of the securities of the Company
then outstanding following such exercise. For purposes of this Section 11(b), the aggregate number of shares of Common Stock or voting securities beneficially owned by the Holder and its Affiliates and any other Persons
whose beneficial ownership of Common Stock would be aggregated with the Holder’s for purposes of Section 13(d) of the Exchange Act shall include the shares of Common Stock issuable upon the exercise of this Warrant with respect to which
such determination is being made, but shall exclude the number of shares of Common Stock which would be issuable upon (x) exercise of the remaining unexercised and non-cancelled portion of this Warrant by
the Holder and (y) exercise or conversion of the unexercised, non-converted or non-cancelled portion of any other securities of the Company that do not have voting
power (including without limitation any securities of the Company which would entitle the holder thereof to acquire at any time Common Stock, including without limitation any debt, preferred stock, right, option, warrant or other instrument that is
at any time convertible into or exercisable or exchangeable for, or otherwise entitles the holder thereof to receive, Common Stock), is subject to a limitation on conversion or exercise analogous to the limitation contained herein and is
beneficially owned by the Holder or any of its Affiliates and other Persons whose beneficial ownership of Common Stock would be aggregated with the Holder’s for purposes of Section 13(d) of the Exchange Act. 

(c) This Section 11 shall not restrict the number of shares of Common Stock which a Holder may receive or
beneficially own in order to determine the amount of securities or other consideration that such Holder may receive in the event of a Fundamental Transaction as contemplated in Section 9 of this Warrant. 

12. No Fractional Shares. No fractional Warrant Shares will be issued in connection with any exercise of this Warrant. In lieu of any fractional shares
that would otherwise be issuable, the number of Warrant Shares to be issued shall be rounded down to the next whole number and the Company shall pay the Holder in cash the fair market value (based on the Closing Sale Price) for any such fractional
shares. 
 13. Notices. Any and all notices or other communications or deliveries hereunder (including, without limitation, any Exercise Notice)
shall be in writing and shall be deemed given and effective on the earliest of (i) the date of transmission, if such notice or communication is delivered via facsimile or confirmed e-mail at the facsimile
number or e-mail address specified below prior to 5:30 P.M., New York City time, on a Trading Day, (ii) the next Trading Day after the date of transmission, if such notice or communication is delivered
via facsimile or confirmed e-mail at the facsimile number or e-mail address specified below on a day that is not a Trading Day or later than 5:30 P.M., New York City time, on any Trading Day, (iii) the
Trading Day following the date of mailing, if sent by nationally recognized overnight courier service specifying next business day delivery, or (iv) upon actual receipt by the Person to whom such notice is required to be given, if by hand
delivery. 
 14. Warrant Agent. The Company shall initially serve as warrant agent under this Warrant. Upon thirty (30) days’ notice to the
Holder, the Company may appoint a new warrant agent. Any corporation into which the Company or any new warrant agent may be merged or any corporation resulting from any consolidation to which the Company or any new warrant agent shall be a party or
any corporation to which the Company or any new warrant agent transfers substantially all of its corporate trust or shareholders services business shall be a successor warrant agent under this Warrant without any further act. Any such successor
warrant agent shall promptly cause notice of its succession as warrant agent to be mailed (by first class mail, postage prepaid) to the Holder at the Holder’s last address as shown on the Warrant Register. 

  
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 15. Miscellaneous. 

(a) No Rights as a Stockholder. The Holder, solely in such Person’s capacity as a holder of this Warrant, shall not be entitled to
vote or receive dividends or be deemed the holder of share capital of the Company for any purpose, nor shall anything contained in this Warrant be construed to confer upon the Holder, solely in such Person’s capacity as the Holder of this
Warrant, any of the rights of a stockholder of the Company or any right to vote, give or withhold consent to any corporate action (whether any reorganization, issue of stock, reclassification of stock, consolidation, merger, amalgamation, conveyance
or otherwise), receive notice of meetings, receive dividends or subscription rights, or otherwise, prior to the issuance to the Holder of the Warrant Shares which such Person is then entitled to receive upon the due exercise of this Warrant. In
addition, nothing contained in this Warrant shall be construed as imposing any liabilities on the Holder to purchase any securities (upon exercise of this Warrant or otherwise) or as a stockholder of the Company, whether such liabilities are
asserted by the Company or by creditors of the Company. 
 (b) Authorized Shares. 

(i) Except and to the extent as waived or consented to by the Holder, the Company shall not by any action, including, without limitation,
amending its certificate or articles of incorporation or through any reorganization, transfer of assets, consolidation, merger, dissolution, issue or sale of securities or any other voluntary action, avoid or seek to avoid the observance or
performance of any of the terms of this Warrant, but will at all times in good faith assist in the carrying out of all such terms and in the taking of all such actions as may be necessary or appropriate to protect the rights of Holder as set forth
in this Warrant against impairment. Without limiting the generality of the foregoing, the Company will (a) not increase the par value of any Warrant Shares above the amount payable therefor upon such exercise immediately prior to such increase
in par value, (b) take all such action as may be necessary or appropriate in order that the Company may validly and legally issue fully paid and nonassessable Warrant Shares upon the exercise of this Warrant, and (c) use commercially
reasonable efforts to obtain all such authorizations, exemptions or consents from any public regulatory body having jurisdiction thereof as may be necessary to enable the Company to perform its obligations under this Warrant. 

(ii) Before taking any action which would result in an adjustment in the number of Warrant Shares for which this Warrant is exercisable or in
the Exercise Price, the Company shall obtain all such authorizations or exemptions thereof, or consents thereto, as may be necessary from any public regulatory body or bodies having jurisdiction thereof. 

(c) Successors and Assigns. Subject to the restrictions on transfer set forth in this Warrant and the restrictions on transfer set
forth in this Warrant and compliance with applicable securities laws, this Warrant may be assigned by the Holder. This Warrant may not be assigned by the Company without the written consent of the Holder except to a successor in the event of a
Fundamental Transaction. This Warrant shall be binding on and inure to the benefit of the Company and the Holder and their respective successors and assigns. Subject to the preceding sentence, nothing in this Warrant shall be construed to give to
any Person other than the Company and the Holder any legal or equitable right, remedy or cause of action under this Warrant. This Warrant may be amended only in writing signed by the Company and the Holder, or their successors and assigns. 

(d) Amendment and Waiver. Except as otherwise provided herein, the provisions of the Warrants may be amended and the Company may take
any action herein prohibited, or omit to perform any act herein required to be performed by it, only if the Company has obtained the written consent of the Holders of Warrants representing no less than a majority of the Warrant Shares obtainable
upon exercise of the Warrants then outstanding. 
 (e) Acceptance. Receipt of this Warrant by the Holder shall constitute acceptance
of and agreement to all of the terms and conditions contained herein. 
 (f) Governing Law; Jurisdiction. ALL QUESTIONS CONCERNING
THE CONSTRUCTION, VALIDITY, ENFORCEMENT AND INTERPRETATION OF THIS WARRANT SHALL BE GOVERNED BY AND CONSTRUED AND ENFORCED IN ACCORDANCE WITH THE LAWS OF THE STATE OF NEW YORK WITHOUT REGARD TO THE PRINCIPLES OF CONFLICTS OF LAW THEREOF. EACH OF THE
COMPANY AND THE HOLDER HEREBY IRREVOCABLY SUBMITS TO THE EXCLUSIVE JURISDICTION OF THE STATE AND FEDERAL COURTS SITTING IN THE CITY OF NEW YORK, BOROUGH OF MANHATTAN, FOR THE ADJUDICATION OF ANY DISPUTE HEREUNDER OR IN CONNECTION HEREWITH OR WITH
ANY TRANSACTION CONTEMPLATED HEREBY OR DISCUSSED HEREIN (INCLUDING WITH RESPECT TO THE ENFORCEMENT OF ANY OF THE TRANSACTION DOCUMENTS), AND HEREBY IRREVOCABLY WAIVES, AND AGREES NOT TO ASSERT IN ANY SUIT, ACTION OR PROCEEDING, ANY CLAIM THAT IT IS
NOT PERSONALLY SUBJECT TO THE JURISDICTION OF ANY SUCH COURT. EACH OF THE COMPANY AND THE HOLDER HEREBY IRREVOCABLY WAIVES PERSONAL SERVICE OF PROCESS AND CONSENTS TO PROCESS BEING SERVED IN ANY SUCH SUIT, ACTION OR PROCEEDING BY MAILING A COPY
THEREOF VIA REGISTERED OR CERTIFIED MAIL OR OVERNIGHT DELIVERY (WITH EVIDENCE OF DELIVERY) TO SUCH PERSON AT THE ADDRESS IN EFFECT 

  
 7 

 
FOR NOTICES TO IT AND AGREES THAT SUCH SERVICE SHALL CONSTITUTE GOOD AND SUFFICIENT SERVICE OF PROCESS AND NOTICE THEREOF. NOTHING CONTAINED HEREIN SHALL BE DEEMED TO LIMIT IN ANY WAY ANY RIGHT
TO SERVE PROCESS IN ANY MANNER PERMITTED BY LAW. EACH OF THE COMPANY AND THE HOLDER HEREBY WAIVES ALL RIGHTS TO A TRIAL BY JURY. 
 (g)
Headings. The headings herein are for convenience only, do not constitute a part of this Warrant and shall not be deemed to limit or affect any of the provisions hereof. 

(h) Severability. In case any one or more of the provisions of this Warrant shall be invalid or unenforceable in any respect, the
validity and enforceability of the remaining terms and provisions of this Warrant shall not in any way be affected or impaired thereby, and the Company and the Holder will attempt in good faith to agree upon a valid and enforceable provision which
shall be a commercially reasonable substitute therefor, and upon so agreeing, shall incorporate such substitute provision in this Warrant. 

[REMAINDER OF PAGE INTENTIONALLY LEFT BLANK] 

  
 8 

 IN WITNESS WHEREOF, the Company has caused this Warrant to be duly executed by its authorized officer as of
the date first indicated above. 
  

			
	SYNDAX PHARMACEUTICALS, INC.

 
			
		
	By:	 	 
	Name:	 	
	Title:	 	

  
 9 

 SCHEDULE 1 

FORM OF EXERCISE NOTICE 
 [To be
executed by the Holder to purchase shares of Common Stock under the Warrant] 
 Ladies and Gentlemen: 

 

	(1)	 The undersigned is the Holder of Warrant No. ___ (the “Warrant”) issued by Syndax
Therapeutics, Inc., a Delaware corporation (the “Company”). Capitalized terms used herein and not otherwise defined herein have the respective meanings set forth in the Warrant. 

 

	(2)	 The undersigned hereby exercises its right to purchase Warrant Shares pursuant to the Warrant.

  

	(3)	 The Holder intends that payment of the Exercise Price shall be made as (check one): 

 

	 	☐	 Cash Exercise 

  

	 	☐	 “Cashless Exercise” under Section 10 of the Warrant 

 

	(4)	 If the Holder has elected a Cash Exercise, the Holder shall pay the sum of
$                in immediately available funds to the Company in accordance with the terms of the Warrant. 

 

	(5)	 Pursuant to this Exercise Notice, the Company shall deliver to the Holder Warrant Shares determined in
accordance with the terms of the Warrant. 

  

	(6)	 By its delivery of this Exercise Notice, the undersigned represents and warrants to the Company that in giving
effect to the exercise evidenced hereby the Holder will not beneficially own in excess of the number of shares of Common Stock (as determined in accordance with Section 13(d) of the Securities Exchange Act of 1934, as amended) permitted to be
owned under Section 11(a) or Section 11(b), as applicable, of the Warrant to which this notice relates. 

  

			
	Dated:	 	 
		
	Name of Holder:	 	 
		
	By:	 	 
	Name:	 	 
	Title:	 	 

 (Signature must conform in all respects to name of Holder as specified on the face of the Warrant)EX-10.1

 Exhibit 10.1 

SECURITIES PURCHASE AGREEMENT 

THIS SECURITIES PURCHASE AGREEMENT (the “Agreement”) is made as of the 30th day of January, 2020, by and among Syndax
Pharmaceuticals, Inc., a Delaware corporation (the “Company”), and the investors set forth on the signature pages hereto (the “Investors”). 

THE PARTIES HEREBY AGREE AS FOLLOWS: 
 1.
Purchase and Sale of Securities. 
 1.1 Sale and Issuance. Subject to the terms and conditions of this Agreement, each
Investor, severally and not jointly, agrees to purchase at the Closing and the Company agrees to sell and issue to such Investor at the Closing the number of shares of the Company’s common stock, $0.0001 par value (the “Common
Stock”) set forth on such Investor’s signature page hereof at a purchase price of $8.00 per share (the “Shares”); provided, however, that, at the option of the Investor, in lieu of purchasing Common
Stock, such Investor may elect to purchase pre-funded warrants to purchase shares of Common Stock with an exercise price of $0.0001 per share (the “Pre-Funded
Warrants”) at a purchase price of $8.00 minus the $0.0001 per share (the Pre-Funded Warrants together with the Shares, the “Securities”). The shares of Common Stock issuable upon
exercise of the Pre-Funded Warrants are referred to herein as the “Warrant Shares.” 

1.2 Closing. The purchase and sale of the Securities shall take place at the offices of Cooley LLP located at 3175 Hanover
Street, Palo Alto, California 94304 at 10:00 A.M. Pacific Time, on February 4, 2020, or at such other time and place as the Company and the Investors may mutually agree upon in writing (which time and place are designated as the
“Closing”). At the Closing, the Company shall (a) cause its transfer agent to deliver to each Investor, via electronic book-entry, the Shares, (b) deliver to each investor the
Pre-Funded Warrants, if applicable, that such Investor is purchasing against payment of the purchase price therefor by wire transfer of immediately available funds to an account specified by the Company in
writing to the Investors, and (c) cause its outside legal counsel, Cooley LLP, to deliver to each Investor a legal opinion in a form to be agreed to between the Company and the Investors. 

2. Representations and Warranties of the Company. The Company hereby represents and warrants to each Investor that: 

2.1 The Company meets the requirements for use of Form S-3 under the Securities Act of 1933, as
amended (the “Securities Act”), and has filed with the Securities and Exchange Commission (the “Commission”) a registration statement on such Form (Registration File
No. 333-233564), which became effective as of September 10, 2019, for the registration under the Securities Act of the Securities and the Warrant Shares. Such registration statement meets the
requirements set forth in Rule 415(a)(1)(x) under the Securities Act and complies with said Rule. The Company will file with the Commission pursuant to Rule 424(b) under the Securities Act, and the rules and regulations (the “Rules and
Regulations”) of the Commission promulgated thereunder, a supplement to the form of prospectus filed with the Commission on August 30, 2019. Such registration statement, including the exhibits thereto, as amended at the date of this
Agreement, is hereinafter called the “Registration Statement”; such prospectus in the form filed 

  
 1 

 
with the Commission on August 30, 2019, is hereinafter called the “Base Prospectus”; and the form of prospectus supplement, in the form in which it will be filed with the
Commission pursuant to Rule 424(b) (including the Base Prospectus as so supplemented) is hereinafter called the “Prospectus Supplement.” Any reference herein to the Registration Statement, the Base Prospectus or the Prospectus
Supplement shall be deemed to refer to and include the documents incorporated by reference therein (the “Incorporated Documents”) pursuant to Item 12 of Form S-3 which were filed under the
Securities Exchange Act of 1934, as amended (the “Exchange Act”), on or before the date of this Agreement, or the issue date of the Base Prospectus or the Prospectus Supplement, as the case may be; and any reference herein to the
terms “amend,” “amendment” or “supplement” with respect to the Registration Statement, the Base Prospectus or the Prospectus Supplement shall be deemed to refer to and include the filing of any document under the
Exchange Act after the date of this Agreement, or the issue date of the Base Prospectus or the Prospectus Supplement, as the case may be, deemed to be incorporated therein by reference. All references in this Agreement to financial statements and
schedules and other information which is “contained,” “included,” “described,” “set forth” or “stated” in the Registration Statement, the Base Prospectus or the Prospectus Supplement (and all other
references of like import) shall be deemed to mean and include all such financial statements and schedules and other information which is or is deemed to be incorporated by reference in the Registration Statement, the Base Prospectus or the
Prospectus Supplement, as the case may be. No stop order suspending the effectiveness of the Registration Statement or the use of the Base Prospectus or the Prospectus Supplement has been issued, and no proceeding for any such purpose is pending or
has been initiated or, to the Company’s knowledge, is threatened by the Commission. 
 2.2 The Registration Statement contains
all exhibits and schedules as required by the Securities Act. Each of the Registration Statement and any post-effective amendment thereto, at the time it became effective, complied in all material respects with the Securities Act and the Exchange
Act and the applicable Rules and Regulations and did not and, as amended or supplemented, if applicable, will not, contain any untrue statement of a material fact or omit to state a material fact required to be stated therein or necessary to make
the statements therein not misleading. The Base Prospectus and the Prospectus Supplement, each as of its respective date, complied in all material respects with the Securities Act and the Exchange Act and the applicable Rules and Regulations. Each
of the Base Prospectus and the Prospectus Supplement, as amended or supplemented, did not and will not contain as of the date thereof any untrue statement of a material fact or omit to state a material fact necessary in order to make the statements
therein, in light of the circumstances under which they were made, not misleading. The Incorporated Documents, when they were filed with the Commission, conformed in all material respects to the requirements of the Exchange Act and the applicable
Rules and Regulations and none of such Incorporated Documents, when they were filed with the Commission, contained any untrue statement of a material fact or omitted to state a material fact necessary to make the statements therein, in light of the
circumstances under which they were made, not misleading; and any further documents so filed and incorporated by reference in the Base Prospectus or Prospectus Supplement, when such documents are filed with the Commission, will conform in all
material respects to the requirements of the Exchange Act and the applicable Rules and Regulations, as applicable, and will not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements
therein, in light of 

  
 2 

 
the circumstances under which they were made, not misleading. Notwithstanding the foregoing, the Company makes no representations or warranties as to information, if any, contained in or omitted
from the Prospectus Supplement or any amendment thereof or supplement thereto in reliance upon and in conformity with information furnished in writing to the Company by or on behalf of any Investor specifically for use in the Registration Statement
or the Prospectus Supplement. No post-effective amendment to the Registration Statement reflecting any facts or events arising after the date thereof which represent, individually or in the aggregate, a fundamental change in the information set
forth therein is required to be filed with the Commission. There are no documents required to be filed with the Commission in connection with the transaction contemplated hereby that have not been filed as required pursuant to the Securities Act or
will not be filed within the requisite time period. 
 2.3 Neither the Company nor any of its directors and officers has distributed
and none of them will distribute, prior to the Closing, any offering material in connection with the offering and sale of the Securities other than the Base Prospectus, the Prospectus Supplement, the Registration Statement, copies of the documents
incorporated by reference therein and any other materials permitted by the Securities Act. 
 2.4 The Company has been duly organized
and is validly existing as a corporation and is in good standing under the laws of the State of Delaware as of the date hereof, and is duly qualified to do business and as in good standing in each other jurisdiction in which its ownership or lease
of property or the conduct of business requires such qualification, except where the failure to qualify, singularly or in the aggregate, would not have or reasonably be expected to result in a material adverse effect on the business, properties,
operations, condition (financial or otherwise) or results of operations of the Company taken as a whole, or in its ability to perform its obligations under this Agreement (a “Material Adverse Effect”). All direct and indirect
subsidiaries of the Company (“Subsidiaries”) are duly organized and in good standing under the laws of the place of organization or incorporation, and each Subsidiary is in good standing in each jurisdiction in which its ownership
or lease of property or the conduct of business requires such qualification, except where the failure to qualify would not have a Material Adverse Effect on the assets, business or operations of the Company taken as a whole. 

2.5 The Company has the requisite corporate power and authority to enter into and to consummate the transactions contemplated by the
Agreement and otherwise to carry out its obligations hereunder. The execution and delivery of the Agreement to which it is a party by the Company and the consummation by it of the transactions contemplated hereby have been duly authorized by all
necessary corporate action on the part of the Company and no further corporate consent or action is required to be obtained by the Company, its Board of Directors or its stockholders in connection therewith other than in connection with the listing
applications with respect to the listing of the Shares, including the Warrant Shares. The Agreement has been (or upon delivery will have been) duly executed by the Company and, when delivered in accordance with the terms hereof, will constitute the
legally valid and binding obligation of the Company enforceable against the Company in accordance with its terms except (i) as limited by general equitable principles and applicable bankruptcy, insolvency, reorganization, moratorium and other
laws of general application affecting enforcement of creditors’ rights generally, (ii) as limited by laws relating to the availability of specific performance, injunctive relief or other equitable remedies and (iii) insofar as
indemnification and contribution provisions may be limited by applicable law. 

  
 3 

 2.6 The Securities have been duly authorized for issuance and sale pursuant to this
Agreement and, when issued and delivered by the Company pursuant to this Agreement, will be validly issued, fully paid and non-assessable, and free and clear of all liens imposed by the Company. The Warrant
Shares have been duly authorized and reserved for issuance and sale pursuant to the terms of the Pre-Funded Warrant, as applicable, and when issued against payment therefor pursuant to the terms of such
warrant, will be validly issued, fully paid and non-assessable, and free and clear of all liens imposed by the Company. 

2.7 The Company and its Board of Directors have taken all necessary action, if any, in order to render inapplicable any control share
acquisition, business combination, poison pill (including any distribution under a rights agreement), or other similar anti-takeover provision pursuant to the Amended and Restated Certificate of Incorporation, the Amended and Restated Bylaws or the
laws of its state of incorporation that is or could become applicable to the Investors as a result of the Investors and the Company fulfilling their obligations or exercising their rights pursuant to the Agreement and the transactions contemplated
hereby, including without limitation, as a result of the Company’s issuance of the Securities and the Investors’ ownership of the Securities. All such anti-takeover provisions in effect as of the date hereof are summarized generally in the
Base Prospectus under the caption, “Description of Capital Stock – Anti-Takeover Provisions.” 
 2.8 All issued and
outstanding securities of the Company issued prior to the transactions contemplated by this Agreement have been duly authorized and validly issued and are fully paid and non-assessable; the holders thereof
have no rights of rescission with respect thereto, and are not subject to personal liability by reason of being such holders; and none of such securities were issued in violation of the preemptive rights of any holders of any security of the Company
or similar contractual rights granted by the Company. 
 2.9 The Common Stock is registered pursuant to Section 12(b) or 12(g)
of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), and the Company has taken no action designed to, or which to its knowledge is likely to have the effect of, terminating the registration of the Common Stock
pursuant to the Exchange Act nor has the Company received any notification that the Commission is currently contemplating terminating such registration. The Company is currently in compliance with all applicable listing and maintenance
requirements of The Nasdaq Stock Market (“Nasdaq”) and, except as disclosed in its filings with the Commission, the Company has not, in the 12 months preceding the date hereof, received notice from Nasdaq to the effect that the
Company is not in compliance with such listing or maintenance requirements. 
 3. Representations and Warranties of the Investor. Each
Investor hereby represents and warrants to the Company that the Investor has full right, power and authority to enter into this Agreement and to consummate the transactions contemplated hereby and has taken all necessary action to authorize the
execution, delivery and performance of this Agreement. This Agreement constitutes a valid and binding obligation of the Investor enforceable against the Investor in accordance with its terms, except as enforceability may be limited by applicable
bankruptcy, insolvency, reorganization, moratorium or similar laws affecting creditors’ and contracting parties’ rights generally and except as enforceability may be subject to general principles of equity (regardless of whether such
enforceability is considered in a proceeding in equity or at law). 

  
 4 

 4. Miscellaneous. 

4.1 Integration. After this transaction, the Company shall not sell, offer for sale or solicit offers to buy or otherwise
negotiate in respect of any security (as defined in Section 2 of the Securities Act) that would be integrated with the offer or sale of the Securities such that the rules of Nasdaq would require stockholder approval of this transaction prior to
the closing of such other transaction unless stockholder approval is obtained before the closing of such subsequent transaction. 

4.2 Successors and Assigns. Except as otherwise provided herein, the terms and conditions of this Agreement shall inure to the
benefit of and be binding upon the respective successors and assigns of the parties. Nothing in this Agreement, express or implied, is intended to confer upon any party other than the parties hereto or their respective successors and assigns any
rights, remedies, obligations, or liabilities under or by reason of this Agreement, except as expressly provided in this Agreement. 

4.3 Governing Law. This Agreement shall be governed by and construed under the laws of the State of New York as applied to
agreements among New York residents entered into and to be performed entirely within New York. 
 4.4 Execution. This
Agreement may be executed in two (2) or more counterparts, all of which when taken together shall be considered one and the same agreement and shall become effective when counterparts have been signed by each party and delivered to each other
party, it being understood that the parties need not sign the same counterpart. In the event that any signature on this Agreement or any instrument pursuant to Section 4.8 hereof is delivered by facsimile transmission or by e-mail delivery of a “.pdf” format data file, such signature shall create a legally valid and binding obligation of the party executing (or on whose behalf such signature is executed) with the same force
and effect as if such facsimile or “.pdf” signature page were an original thereof. 
 4.5 Titles and Subtitles. The
titles and subtitles used in this Agreement are used for convenience only and are not to be considered in construing or interpreting this Agreement. 

4.6 Notices. Unless otherwise provided, any notice required or permitted under this Agreement shall be given in writing and
shall be deemed effectively given upon personal delivery to the party to be notified or upon deposit with the United States Post Office, by registered or certified mail, postage prepaid and addressed to the party to be notified at the address
indicated for such party on the signature page hereof, or at such other address as such party may designate by ten (10) days’ advance written notice to the other parties. 

  
 5 

 4.7 Finder’s Fee. Each party represents that it neither is nor will be
obligated for any finders’ fee or commission in connection with this transaction. Each Investor agrees to indemnify and to hold harmless the Company from any liability for any commission or compensation in the nature of a finders’ fee (and
the costs and expenses of defending against such liability or asserted liability) for which such Investor or any of its officers, partners, employees, or representatives is responsible. The Company agrees to indemnify and hold harmless each Investor
from any liability for any commission or compensation in the nature of a finders’ fee (and the costs and expenses of defending against such liability or asserted liability) for which the Company or any of its officers, employees or
representatives is responsible. 
 4.8 Amendments and Waivers. Any term of this Agreement may be amended and the observance of
any term of this Agreement may be waived (either generally or in a particular instance and either retroactively or prospectively), only with the written consent of the Company and each Investor. 

4.9 Severability. If one or more provisions of this Agreement are held to be unenforceable under applicable law, such provision
shall be excluded from this Agreement and the balance of the Agreement shall be interpreted as if such provision were so excluded and shall be enforceable in accordance with its terms. 

4.10 Entire Agreement. This Agreement and the other documents referred to herein constitute the entire agreement among the
parties and no party shall be liable or bound to any other party in any manner by any warranties, representations, or covenants except as specifically set forth herein or therein. 

4.11 Indemnification. Subject to the provisions of this Section 4.11, the Company will indemnify and hold each Investor and
its directors, officers, shareholders, members, partners, employees and agents (and any other persons with a functionally equivalent role of a person holding such titles notwithstanding a lack of such title or any other title), each person who
controls such Investor (within the meaning of Section 15 of the Securities Act and Section 20 of the Exchange Act), and the directors, officers, shareholders, agents, members, partners or employees (and any other persons with a
functionally equivalent role of a person holding such titles notwithstanding a lack of such title or any other title) of such controlling persons (each, a “Investor Party”) harmless from any and all losses, liabilities, obligations,
claims, contingencies, damages, costs and expenses, including all judgments, amounts paid in settlements, court costs and reasonable attorneys’ fees and costs of investigation that any such Investor Party may suffer or incur as a result of or
relating to (a) any breach of any of the representations, warranties, covenants or agreements made by the Company in this Agreement or (b) any action instituted against an Investor, or any of them or their respective affiliates, by any
stockholder of the Company who is not an affiliate of such Investor or any governmental or regulatory agency, with respect to any of the transactions contemplated by this Agreement (unless such action is based upon a material breach of such
Investor’s representations, warranties or covenants in this Agreement or any material violations by the Investor of state or federal securities laws or any conduct by such Investor which constitutes fraud, gross negligence, willful misconduct
or malfeasance). If any action shall be brought against any Investor Party in respect of which indemnity may be sought pursuant to this Agreement, such Investor Party shall promptly notify the Company in writing, and the Company shall have the right
to assume the defense thereof with counsel of its own choosing reasonably acceptable to the Investor Party. Any Investor Party shall have the right to engage separate counsel in any such action and 

  
 6 

 
participate in the defense thereof, but the fees and expenses of such counsel shall be at the expense of such Investor Party except to the extent that (i) the engagement thereof has been
specifically authorized by the Company in writing, (ii) the Company has failed after a reasonable period of time to assume such defense and to employ counsel or (iii) in such action there is, in the reasonable opinion of such separate
counsel, a material conflict on any material issue between the position of the Company and the position of such Investor Party, in which case the Company shall be responsible for the reasonable fees and expenses of no more than one such separate
counsel. The Company will not be liable to any Investor Party under this Agreement (i) for any settlement by a Investor Party effected without the Company’s prior written consent, which shall not be unreasonably withheld or delayed or
(ii) to the extent, but only to the extent, that a loss, claim, damage or liability is attributable to any Investor Party’s breach of any of the representations, warranties, covenants or agreements made by such Investor Party in this
Agreement. To the extent that an Investor Party wishes to seek indemnification under this Section 4.11, such Investor Party must provide the Company with written notice asserting a claim under this Section 4.11, with such notice to be
provided within one year from the Closing. If an Investor Party fails to provide such written notice within this one year period, the Investor Party shall no longer be entitled to indemnification by the Company hereunder. 

4.12 Expenses. Each party shall pay the fees and expenses of its advisers, counsel, accountants and other experts, if any, and
all other expenses incurred by such party incident to the negotiation, preparation, execution, delivery and performance of this Agreement; provided, however, that the Company shall pay the Investors’ reasonable legal fees and
expenses incurred in connection with the transactions contemplated by this Agreement (including any post-Closing expenses) up to an aggregate amount of $25,000. The Company shall pay all transfer agent fees, stamp taxes and other taxes and duties
levied in connection with the delivery of the Securities to the Investors. 
 4.13 Construction. The parties agree that each
of them and/or their respective counsel has reviewed and had an opportunity to revise the Agreement and, therefore, the normal rule of construction to the effect that any ambiguities are to be resolved against the drafting party shall not be
employed in the interpretation of the Agreement or any amendments hereto. 
 [Signature Pages Follow] 

  
 7 

 IN WITNESS WHEREOF, the parties hereto
have executed this Securities Purchase Agreement as of the day and year first above written. 
  

			
	SYNDAX PHARMACEUTICALS, INC.
		
	By:	 	/s/ Luke J. Albrecht
	Name:	 	Luke J. Albrecht
	Title:	 	General Counsel and Corporate Secretary
	Address:	 	35 Gatehouse Drive, Building D, Floor 3
		 	Waltham, Massachusetts

  
 [Company Signature
Page to Purchase Agreement] 

 IN WITNESS WHEREOF, the parties hereto
have executed this Securities Purchase Agreement as of the day and year first above written. 
 Name of Investor: Biotechnology Value Fund, L.P. 

Signature of Authorized Signatory of Investor: /s/
Mark Lampert                             

Name of Authorized Signatory: Mark Lampert 
 Title of Authorized
Signatory: Chief Executive Officer BVF I GP LLC, itself General Partner of Biotechnology Value Fund, L.P. 
 Email Address of Authorized Signatory: [
                ] 
 Address for Notice of Investor: 44 Montgomery Street,
40th Floor, San Francisco, CA 94104 
 Telephone: [                ] 

With a copy to (which shall not constitute notice): 
 Gibson,
Dunn & Crutcher, LLP 
 555 Mission Street, Suite 3000 

San Francisco, CA 94105 
 Attn: Ryan A. Murr 

Address for delivery of Shares via electronic book entry for Investor (if not same as address for notice):
[                     ] 
 Number of Shares to Be
Purchased: 276,095 
 Number of Pre-Funded Warrants:    366,458 

Total Purchase Price: $5,140,387.35 

 IN WITNESS WHEREOF, the parties hereto
have executed this Securities Purchase Agreement as of the day and year first above written. 
 Name of Investor: Biotechnology Value Fund II, L.P. 

Signature of Authorized Signatory of Investor: /s/ Mark
Lampert                         

Name of Authorized Signatory: Mark Lampert 
 Title of Authorized
Signatory: Chief Executive Officer BVF II GP LLC, itself General Partner of Biotechnology Value Fund II, L.P. 
 Email Address of Authorized Signatory:
[                 ] 
 Address for Notice of Investor: 44 Montgomery Street,
40th Floor, San Francisco, CA 94104 
 Telephone: [                ] 

With a copy to (which shall not constitute notice): 
 Gibson,
Dunn & Crutcher, LLP 
 555 Mission Street, Suite 3000 

San Francisco, CA 94105 
 Attn: Ryan A. Murr 

[                     ] 

Number of Shares to Be Purchased: 40,942 
 Number of Pre-Funded Warrants:    209,615 
 Total Purchase Price: $2,004,435.04 

 IN WITNESS WHEREOF, the parties hereto
have executed this Securities Purchase Agreement as of the day and year first above written. 
 Name of Investor: Biotechnology Value Trading Fund OS, L.P.

 Signature of Authorized Signatory of Investor: /s/ Mark
Lampert                         

Name of Authorized Signatory: Mark Lampert 
 Title of Authorized
Signatory: President of BVF, Inc., General Partner of BVF Partners L.P., itself sole member of BVF Partners OS, Ltd., itself GP of Biotechnology Value Trading Fund OS, L.P. 

Email Address of Authorized Signatory: [                 ] 

Address for Notice of Investor: 44 Montgomery Street 40th Floor, San Francisco, CA 94104 

Telephone: [                ] 

With a copy to (which shall not constitute notice): 
 Gibson,
Dunn & Crutcher, LLP 
 555 Mission Street, Suite 3000 

San Francisco, CA 94105 
 Attn: Ryan A. Murr 

[                     ] 

Number of Shares to Be Purchased: 57,963 
 Number of Pre-Funded Warrants:    36,427 
 Total Purchase Price: $755,116.36 

 IN WITNESS WHEREOF, the parties hereto
have executed this Securities Purchase Agreement as of the day and year first above written. 
 Name of Investor: MSI BVF SPV, L.L.C. 

Signature of Authorized Signatory of Investor: /s/ Mark
Lampert                         

Name of Authorized Signatory: Mark Lampert 
 Title of Authorized
Signatory: President of BVF, Inc., itself GP of BVF Partners L.P., itself attorney-in-fact for MSI BVF SPV, L.L.C. 

Email Address of Authorized Signatory: [             ] 

Address for Notice of Investor: 44 Montgomery Street, 40th Floor, San Francisco, CA 94104 

Telephone: [                    ] 

With a copy to (which shall not constitute notice): 
 Gibson,
Dunn & Crutcher, LLP 
 555 Mission Street, Suite 3000 

San Francisco, CA 94105 
 Attn: Ryan A. Murr 

Address for delivery of Shares via electronic book entry for Investor (if not same as address for notice):
[                     ] 
 Number of Shares to Be
Purchased: 
 Number of Pre-Funded Warrants: 

Total Purchase Price: 

 IN WITNESS WHEREOF, the parties hereto
have executed this Securities Purchase Agreement as of the day and year first above written. 
 Name of Investor: Access Industries Holdings LLC 

Signature of Authorized Signatory of Investor: /s/ Avi
Naider                         

Name of Authorized Signatory: Avi Naider 
 Title of Authorized
Signatory: President of AI LSI Management, LLC, Manager of Investor 
 Email Address of Authorized Signatory: [
                ] 
 Address for Notice of Investor: c/o Access Industries,
Inc., 40 West 57th Street, 28th Floor, New York, New York 10019 

Telephone: [                ] 

With a copy to: 
 Access Industries, Inc. 

40 West 57th Street, 28th Floor 

New York, New York 10019 
 Attention: Legal Department; Langhorne
Perrow 
 Email: [                     ] 

With a copy to (which shall not constitute notice): 
 Gibson,
Dunn & Crutcher, LLP 
 555 Mission Street, Suite 3000 

San Francisco, CA 94105 
 Attn: Ryan A. Murr 

Address for delivery of Shares via electronic book entry for Investor (if not same as address for notice): 

Number of Shares to Be Purchased: 1,000,000 
 Number of Pre-Funded Warrants: 2500,000 
 Total Purchase Price: $9,999,975.00 

 IN WITNESS WHEREOF, the parties hereto
have executed this Securities Purchase Agreement as of the day and year first above written. 
 Name of Investor: Aisling Capital V, LP 

Signature of Authorized Signatory of Investor: /s/ Robert
Wenzel                         

Name of Authorized Signatory: Robert Wenzel 
 Title of Authorized
Signatory: CFO 
 Email Address of Authorized Signatory: [                 ]

 Address for Notice of Investor: 888 7th Avenue,
12th floor, NY, NY 10106 
 Telephone:
[                ] 
 With a copy to (which shall not constitute notice):

 McDermott Will & Emery LLP 
 340 Madison
Avenue 
 New York, NY 10173 
 Attn: Todd Finger 

Address for delivery of Shares via electronic book entry for Investor (if not same as address for notice): 

[                ] 

Number of Shares to Be Purchased: 875,000 
 Number of Pre-Funded Warrants: - 
 Total Purchase Price: $7,000,000.00 

[Investor Signature Page to Purchase Agreement] 

 IN WITNESS WHEREOF, the parties hereto
have executed this Securities Purchase Agreement as of the day and year first above written. 
 Name of Investor: Boxer Capital, LLC 

Signature of Authorized Signatory of Investor: /s/ Aaron
Davis                         

Name of Authorized Signatory: Aaron Davis 
 Title of Authorized
Signatory: Chief Executive Officer 
 Email Address of Authorized Signatory: [
                 ] 
 Address for Notice of Investor: 11682 El Camino Real,
Suite 320, San Diego, CA 92130 
 Telephone: [                ] 

Address for delivery of Shares via electronic book entry for Investor (if not same as address for notice): 

Number of Shares to Be Purchased: 475,782 
 Number of Pre-Funded Warrants: 475,787 
 Total Purchase Price: $7,612,504.43 

[Investor Signature Page to Purchase Agreement] 

 IN WITNESS WHEREOF, the parties hereto
have executed this Securities Purchase Agreement as of the day and year first above written. 
 Name of Investor: 683 CAPITAL PARTNERS, LP 

Signature of Authorized Signatory of Investor: /s/ Ari
Zweiman                         

Name of Authorized Signatory: Ari Zweiman 
 Title of Authorized
Signatory: Portfolio Manager 
 Email Address of Authorized Signatory:
[                 ] 
 Address for Notice of Investor: 3 Columbus Circle,
Suite 2205, New York, NY 10019 
 Telephone: [                ] 

Address for delivery of Shares via electronic book entry for Investor (if not same as address for notice): 

Number of Shares to Be Purchased: 250,000 
 Number of Pre-Funded Warrants: 
 Total Purchase Price: 2,000,000.00 

[Investor Signature Page to Purchase Agreement] 

 IN WITNESS WHEREOF, the parties hereto
have executed this Securities Purchase Agreement as of the day and year first above written. 
 Name of Investor: MVA Investors, LLC 

Signature of Authorized Signatory of Investor: /s/ Aaron
Davis                         

Name of Authorized Signatory: Aaron Davis 
 Title of Authorized
Signatory: Chief Executive Officer 
 Email Address of Authorized Signatory: [
                ] 
 Address for Notice of
Investor:    11682 El Camino Real, Suite 320, San Diego, CA 92130 
 Telephone:
[            ] 
 Address for delivery of Shares via electronic book entry for Investor (if not
same as address for notice): 
 Number of Shares to Be Purchased: 48,437 

Number of Pre-Funded Warrants: 

Total Purchase Price: $387,496.00 

[Investor Signature Page to Purchase Agreement] 

 IN WITNESS WHEREOF, the parties hereto
have executed this Securities Purchase Agreement as of the day and year first above written. 
 Name of Investor: Briggs W. Morrison, M.D. 

Signature of Authorized Signatory of Investor: /s/ Briggs
Morrison                         

Name of Authorized Signatory: Briggs Morrison 
 Title of
Authorized Signatory: 
 Email Address of Authorized Signatory: [              ] 

Address for Notice of Investor: [                ] 

Telephone: [                    ] 

Address for delivery of Shares via electronic book entry for Investor (if not same as address for notice): 

Number of Shares to Be Purchased: 12,500 
 Number of Pre-Funded Warrants: 
 Total Purchase Price: $100,000 

[Investor Signature Page to Purchase Agreement]

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