Document:

<Page>

                                                                     EXHIBIT 4.1

                                         COMMON STOCK
                              THIS CERTIFICATE IS TRANSFERABLE
                              IN CANTON, MA AND JERSEY CITY, NJ

COMMON STOCK
PAR VALUE, $0.0001

Certificate Number                                                        Shares

ZQ                                [LOGO] SYNTA
                                PHARMACEUTICALS

                                                              CUSIP 87162T 20 6

                                                               SEE REVERSE FOR
                                                             CERTAIN DEFINITIONS

                          SYNTA PHARMACEUTICALS CORP.
                          INCORPORATED UNDER THE LAWS
                            OF THE STATE OF DELAWARE

--------------------------------------------------------------------------------
THIS CERTIFIES THAT

is the owner of

--------------------------------------------------------------------------------

             FULLY PAID AND NON-ASSESSABLE SHARES OF COMMON STOCK,
                         PAR VALUE $0.0001 PER SHARE, OF

===========================SYNTA PHARMACEUTICALS CORP.==========================

transferable on the books of the Corporation by the holder hereof in person
or by duly authorized attorney upon surrender of this certificate properly
endorsed. This certificate is not valid unless countersigned and registered
by the Transfer Agent and Registrar.

     WITNESS the facsimile seal of the Corporation and the facsimile signatures
of its duly authorized officers.

                          SYNTA PHARMACEUTICALS CORP.
                                      2000
                                    Delaware

                                     [SEAL]

      /s/ Safi R. Bahcall
President and Chief Executive Officer

     /s/ Keith S. Ehrlich
Vice President, Chief Financial Officer and Treasurer

DATED

COUNTERSIGNED AND REGISTERED:
           COMPUTERSHARE TRUST COMPANY,N.A.
                                 TRANSFER AGENT
                                  AND REGISTRAR
BY

                           AUTHORIZED SIGNATURE

<Page>

THE CORPORATION WILL FURNISH WITHOUT CHARGE TO EACH STOCKHOLDER WHO SO
REQUESTS A STATEMENT OF THE POWERS, DESIGNATIONS, PREFERENCES AND RELATIVE,
PARTICIPATING, OPTIONAL, OR OTHER SPECIAL RIGHTS OF EACH CLASS OF STOCK OR
SERIES THEREOF OF THE CORPORATION, AND THE QUALIFICATIONS, LIMITATIONS OR
RESTRICTIONS OF SUCH PREFERENCES AND/OR RIGHTS.

The following abbreviations, when used in the inscription on the face of this
certificate, shall be construed as though they were written out in full
according to applicable laws or regulations:

TEN COM   --   as tenants in common
TEN ENT   --   as tenants by the entireties
JT TEN    --   as joint tenants with right of
               survivorship and not as tenants
               in common

UNIF GIFT MIN ACT -.........................Custodian........................
                           (Cust)                            (Minor)

                   under Uniform Gifts to Minors Act........................
                                                             (State)

UNIF TRF MIN ACT .................. Custodian (until age ...) ...........
                      (Cust)                                    (Minor)

under Uniform Transfers to Minors Act ............
                                         (State)

    Additional abbreviations may also be used though not in the above list.

For value received,___________________________________hereby sell, assign and
transfer unto

PLEASE INSERT SOCIAL SECURITY OR OTHER
   IDENTIFYING NUMBER OF ASSIGNEE
--------------------------------------

--------------------------------------

________________________________________________________________________________
 (PLEASE PRINT OR TYPEWRITE NAME AND ADDRESS, INCLUDING POSTAL ZIP CODE, OF
 ASSIGNEE)

<Page>

________________________________________________________________________________

________________________________________________________________________________

__________________________________________________________________________Shares

of the capital stock represented by the within certificate, and do hereby
irrevocably constitute and appoint

________________________________________________________________________Attorney

to transfer the said stock on the books of the within named corporation with
full power of substitution in the premises.

Dated ______________________________ 20 _________________________

                       Signature: ______________________________

                               _________________________________________________
                       Notice: the signature to this assignment must correspond
                               with the name as written upon the face of the
                               certificate in every particular, without
                               alteration or enlargement, or any change
                               whatever.

Signature(s) Guaranteed: Medallion Guarantee Stamp

THE SIGNATURE(S) SHOULD BE GUARANTEED BY AN ELIGIBLE GUARANTOR INSTITUTION
(banks, stockbrokers, savings and loan associations and credit unions) WITH
MEMBERSHIP IN AN APPROVED SIGNATURE GUARANTEE MEDALLION PROGRAM, PURSUANT TO
S.E.C. RULE 17Ad-15.

-----------------------------------------------------------------------------
SECURITY INSTRUCTIONS

THIS IS WATERMARKED PAPER. DO NOT ACCEPT WITHOUT NOTING WATERMARK. HOLD TO
LIGHT TO VERIFY WATERMARK.
-----------------------------------------------------------------------------<Page>

                                                                   EXHIBIT 4.2.3

                           SYNTA PHARMACEUTICALS CORP.

                                SECOND AMENDMENT
                                     TO THE
                 AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT

     This Second Amendment (the "AMENDMENT") to the Amended and Restated
Investor Rights Agreement, dated December 13, 2002, as amended by the First
Amendment to the Amended and Restated Investor Rights Agreement, dated January
11, 2005, by and among Synta Pharmaceuticals Corp., a Delaware corporation (the
"COMPANY"), and the Investors named therein (collectively, the "INVESTOR RIGHTS
AGREEMENT"), is made as of January 31, 2007, by and among the Company and the
Investors. Capitalized terms used herein but not defined shall have the meanings
ascribed to such terms in the Investor Rights Agreement.

     WHEREAS, Section 4 of the Investor Rights Agreement sets forth certain
rights granted to the Investors with respect to the right of first refusal (the
"RIGHT OF FIRST REFUSAL") to purchase New Securities, as defined in Section 1(k)
of the Investor Rights Agreement, issued by the Company and the obligation of
the Company to provide notice to the Investors of any such issuances;

     WHEREAS, clauses (i) through (vii) of Section 1(k) of the Investor Rights
Agreement exclude from the definition of New Securities certain securities
issued by the Company;

     WHEREAS, on March 15, 2006, the Company adopted the Synta Pharmaceuticals
Corp. 2006 Stock Plan (the "2006 STOCK PLAN"), pursuant to which the Company has
issued securities to Participants, as defined in the 2006 Stock Plan, from such
adoption through the date hereof (the "2006 STOCK PLAN ISSUANCES"), and intends
to issue additional securities in accordance with the terms of the 2006 Stock
Plan;

     WHEREAS, the 2006 Stock Plan Issuances may give rise to the Investors'
Right of First Refusal with respect to such issuances and the Company's
obligation to provide notice thereof;

     WHEREAS, the Company and the Investors wish to amend the Investor Rights
Agreement by amending the definition of New Securities to exclude all securities
issued under any equity compensation plans approved by the Board of Directors of
the Company from the definition thereof;

     WHEREAS, the Investors wish to waive the Right of First Refusal with
respect to the 2006 Stock Plan Issuances and the Company's obligation to provide
notice thereof; and

     WHEREAS, in accordance with Section 5.7 of the Investor Rights Agreement,
by executing and delivering this Amendment, the Company and each Investor has
approved this Amendment.

     NOW, THEREFORE, in consideration of the premises and the mutual covenants
contained in this Amendment and for other good and valuable consideration, the
receipt and sufficiency of which are hereby acknowledged, the parties hereto
agree as follows:

<Page>

     1. AMENDMENT OF INVESTOR RIGHTS AGREEMENT.

     The Investor Rights Agreement is hereby amended by deleting clause (iii) of
Section 1(k) in its entirety and by substituting in lieu thereof the following:

     "(iii) up to 23,172,930 shares of Common Stock issued or issuable to
     employees, consultants or directors of the Company pursuant to equity
     compensation plans or arrangements approved by the Board of Directors of
     the Company (including shares issued or issuable upon exercise of options
     previously granted), which number of shares (A) shall be adjusted upwards
     to accommodate any increases in the number of shares of Common Stock
     issuable under such plans and arrangements pursuant to the express terms
     and provisions thereof (for example, pursuant to any "evergreen" or similar
     provision set forth in such plans or arrangements) or (B) may be adjusted
     upward by the affirmative vote of the Board of Directors of the Company;"

     2. WAIVER OF RIGHT OF FIRST REFUSAL.

     In accordance with Section 5.7 of the Investor Rights Agreement, the
undersigned Investors, being all of the Investors that are a party to the
Investor Rights Agreement, hereby waive the Right of First Refusal in connection
with the 2006 Stock Plan Issuances of the Company up through and including the
date of this Amendment and the obligation of the Company to provide notice
thereof.

     3. MISCELLANEOUS.

     (i) Except as contemplated by this Amendment, all of the terms and
conditions of the Investor Rights Agreement shall remain in full force and
effect.

     (ii) This Amendment may be executed in one or more counterparts, each of
which shall be deemed an original, but all of which together shall constitute
one and the same instrument.

     REMAINDER OF PAGE INTENTIONALLY LEFT BLANK

                                       2

<Page>

     IN WITNESS WHEREOF, the undersigned have executed this Amendment as of the
date first above written.

                                    COMPANY:

                                    SYNTA PHARMACEUTICALS CORP.

                                    By: /s/ SAFI R. BAHCALL
                                       -----------------------------------------
                                    Name: Safi R. Bahcall, Ph.D.
                                    Title: President and Chief Executive Officer

                                       3

<Page>

     [Second Amendment to the Amended and Restated Investor Rights Agreement,
                           Signature Page, CONTINUED]

                                                     INVESTORS:

                                                     CxSYNTA LLC

                                                     By: /s/ BRUCE KOVNER
                                                         ----------------
                                                     Name: Bruce Kovner
                                                     Title:

                                                     /s/ BRUCE KOVNER
                                                         ------------
                                                     Bruce Kovner

                                                     GOLLUST TRUST II

                                                     By: /s/ KENNETH S. DAVIDSON
                                                         -----------------------
                                                     Name: Kenneth S. Davidson
                                                     Title:

                                                     WYANDANCH PARTNERS, L.P.

                                                     By: /s/ KEITH R. GOLLUST
                                                         --------------------
                                                     Name: Keith R. Gollust
                                                     Title:

                                                     /s/ KEITH R. GOLLUST
                                                         ----------------
                                                     Keith R. Gollust

                                                     /s/ ROBERT A. DAY
                                                         -------------
                                                     Robert A. Day

                                                     ROBERT A. DAY TRUST

                                                     By: /s/ ROBERT A. DAY
                                                         -----------------
                                                     Name: Robert A. Day
                                                     Title

                                       4

<Page>

    [Second Amendment to the Amended and Restated Investor Rights Agreement,
                           Signature Page, CONTINUED]

                                                     /s/ RICHARD N. FOSTER
                                                         -----------------
                                                     Richard N. Foster

                                                     /s/ JONATHAN D. JAFFREY
                                                         -------------------
                                                     Jonathan D. Jaffrey

                                                     /s/ KASHIF F. SHEIKH
                                                         ----------------
                                                     Kashif F. Sheikh

                                       5

Source: [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00116-of-00352.parquet"}, [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00116-of-00352.parquet"}]]