Document:

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                                                                     EXHIBIT 4.5

THIS WARRANT HAS NOT BEEN REGISTERED UNDER THE SECURIITIES ACT OF 1933, AS
AMENDED, OR ANY STATE SECURITIES LAWS. NO SALE OR DISPOSITION MAY BE EFFECTED
WITHOUT (i) EFFECTIVE REGISTRATION STATEMENTS RELATED THERETO, (ii) AN OPINION
OF COUNSEL OR OTHER EVIDENCE, REASONABLY SATISFACTORY TO THE COMPANY, THAT SUCH
REGISTRATIONS ARE NOT REQUIRED, (iii) RECEIPT OF NO-ACTION LETTERS FROM THE
APPROPRIATE GOVERNMENTAL AUTHORITIES, OR (iv) OTHERWISE COMPLYING WITH THE
PROVISIONS OF SECTION 7 OF THIS WARRANT.

                        EXELIXIS PHARMACEUTICALS, INC.

                              WARRANT TO PURCHASE
                           SHARES OF PREFERRED STOCK

          THIS CERTIFIES THAT, for value received, and subject to the provisions
and upon the terms and conditions hereinafter set forth, MMC/GATX PARTNERSHIP
NO. I and its assignees are entitled to subscribe for and purchase up to 357,143
shares of the fully paid and nonassessable shares of Preferred Stock (as
adjusted pursuant to Section 4 hereof, the "Shares") of EXELIXIS
PHARMACEUTICALS, INC., a Delaware corporation (the "Company") at the price per
share (such price and such other price as shall result, from time to time, from
the adjustments specified in Section 4 hereof is herein referred to as the
"Warrant Price") as shall be determined in accordance with Section 1 (a) hereof.
The Preferred Stock issuable hereunder shall be shares of the series of
Preferred Stock (expected to be Series B Preferred Stock) issued to investors in
a financing having aggregate net proceeds in excess of $4,000,000 (whether in
one transaction or in a series of transactions after the date of this Warrant
and excluding the conversion of debt to equity) (a "Qualified Financing");
provided, that if no Qualified Financing occurs prior to April 30, 1996, then
the Preferred Stock issuable hereunder shall be Series A Preferred Stock.  As
used herein, (a) the term "Series Preferred" shall mean the Company's presently
authorized Series A Preferred Stock or contemplated Series B Preferred Stock (as
determined pursuant to the preceding sentence), and any stock into or for which
such Series A Preferred Stock or Series B Preferred Stock, as applicable, may
hereinafter be converted or exchanged, (b) the term "Date of Grant" shall mean
the date as set forth on the signature page hereof; and (c) the term "Other
Warrants" shall mean any other warrants issued by the Company in connection with
the transaction with respect to which this Warrant was issued, and any warrant
issued upon transfer or partial exercise of this Warrant.  The term "Warrant" as
used herein shall be deemed to include Other Warrants unless the context clearly
requires otherwise.

     1.   Warrant Price: Term

          (a) Warrant Price.  The Warrant Price shall be determined as follows:

              (i) If the Company completes a Qualified Financing on or prior to
April 30, 1996, and the price paid by investors in such Qualified Financing is
less than $1.00 per share, then the Warrant Price shall be determined by using
the following formula:

                  Exercise Price = X + Y
                                   _____
                                     2

                                       1.
<PAGE>

Where:    X = The price per share of the Series A Preferred Stock (i.e., $0.70).

          Y = The price per share of the Series B Preferred Stock in a Qualified
              Financing

              (ii)  If the Company does not complete a Qualified Financing on or
prior to April 30, 1996, then the Warrant Price shall be $.70.

              (iii) If the Company does complete a Qualified Financing prior to
April 30, 1995, but the price paid by investors in such financing is equal to or
greater than $1.00 per share, then, the Warrant Price shall be $0.85 per share.

          (b) Term. The purchase right represented by this Warrant is
exercisable, in whole or in part, at anytime and from time to time from the Date
of Grant through the later of (i) ten (10) years after the Date of Grant or (ii)
five (5) years after the closing of the Company's initial public offering of its
Common Stock effected pursuant to a Registration Statement on Form S-I (or its
successor) filed under the Securities Act of 1933, as amended (the "Act").

     2.   Method of Exercise: Payment: Issuance of New Warrant.  Subject to
Section 1 hereof the purchase right represented by this Warrant may be exercised
by the holder hereof in whole or in part and from time to time, at the election
of the holder hereof, (a) the surrender of this Warrant (with the notice of
exercise substantially in the form attached hereto as Exhibit A duly completed
and executed) at the principal office of the Company and by the payment to the
Company, by certified or bank check, or by wire transfer to an account
designated by the Company (a "Wire Transfer") of an amount equal to the then
applicable Warrant Price multiplied by the number of Shares then being
purchased, or (b) if in connection with a registered public offering of the
Company's securities, the surrender of this Warrant (with the notice of exercise
form attached hereto as Exhibit A-I duly completed and executed) at the
principal office of the Company together with notice of arrangements reasonably
satisfactory to the Company for payment to the Company either by certified or
bank check or by Wire Transfer from the proceeds of the sale of shares to be
sold by the holder in such public offering of an amount equal to the then
applicable Warrant Price per share multiplied by the number of Shares then being
purchased, or (c) exercise of the right provided for in Section 10.3 hereof.
The person or persons in whose name(s) any certificate(s) representing shares of
Series Preferred shall be issuable upon exercise of this Warrant be deemed to
have become the holder(s) of record of, and shall be treated for all purposes as
the record holder(s) of, the shares represented thereby (and such shares shall
be deemed to have been issued) immediately prior to the close of business on the
date or dates upon which this Warrant is exercised.  In the event of any
exercise of the rights represented by this Warrant, certificates for the shares
of stock so purchased shall be delivered to the holder hereof as soon as
possible and in any event within thirty (30) days alter such exercise and,
unless this Warrant has been fully exercised or expired, a new Warrant
representing the portion of the Shares, if any, with respect to which this
Warrant shall not then have been exercised shall also be issued to the holder
hereof as soon as possible and in any event within such thirty-day period.

     3.   Stock Fully Paid; Reservation of Shares.  All Shares that may be
issued upon the exercise of the rights represented by this Warrant will, upon
issuance pursuant to the terms and conditions herein, be fully paid and
nonassessable, and free from all taxes, liens and charges

                                       2.
<PAGE>

with respect to the issue thereof. During the period within which the rights
represented by this Warrant may be exercised, the Company will at all times have
authorized, and reserved for the purpose of the issue upon exercise of the
purchase rights evidenced by this Warrant, a sufficient number of shares of its
Series Preferred to provide for the exercise of the rights represented by this
Warrant and a sufficient number of shares of its Common Stock to provide for the
conversion of the Series Preferred into Common Stock.

     4.   Adjustment of Warrant Price and Number of Shares.  The number and kind
of securities purchasable upon the exercise of this Warrant and the Warrant
Price shall be subject to adjustment from time to time upon the occurrence of
certain events, as follows:

          (a) Reclassification or Merger. In case of any reclassification or
change of securities of the class issuable upon exercise of this Warrant (other
than a change in par value, or from par value to no par value, or from no par
value to par value, or as a result of a subdivision or combination), or in case
of any merger of the Company with or into another corporation (other than a
merger with another corporation in which the Company is the acquiring and the
surviving corporation and which does not result in any reclassification or
change of outstanding securities issuable upon exercise of this Warrant), or in
case of any sale of all or substantially all of the assets of the Company, the
Company, or such successor or purchasing corporation, as the case may be, shall
duly execute and deliver to the holder of this Warrant a new Warrant (in form
and substance satisfactory to the holder of this Warrant), so that the holder of
this Warrant shall have the right to receive, at a total purchase price not to
exceed that payable upon the exercise of the unexercised portion of this
Warrant, and in lieu of the shares of Series Preferred theretofore issuable upon
exercise of this Warrant, the kind and amount of shares of stock, other
securities, money and property receivable upon such reclassification, change or
merger by a holder of the number of shares of Series Preferred then purchasable
under this Warrant. Such new Warrant shall provide for adjustments that shall be
as nearly equivalent as may be practicable to the adjustments provided for in
this Section 4 and, in the case of a new Warrant issuable after conversion of
the authorized shares of the Series Preferred into shares of Common Stock or
after the amendment of the terms of the antidilution protection of the Series
Preferred, shall provide for antidilution protection that shall be as nearly
equivalent as may be practicable to the antidilution provisions applicable to
the Series Preferred on the Date of Grant. The provisions of this subparagraph
(a) shall similarly apply to successive reclassifications, changes, mergers and
transfers.

          (b) Subdivision or Combination of Shares. If the Company at any time
while this Warrant remains outstanding and unexpired shall subdivide or combine
its outstanding shares of Series Preferred, the Warrant Price shall be
proportionately decreased in the ease of a subdivision or incurred in the case
of a combination, effective at the close of business on the date the subdivision
or combination becomes effective.

          (c) Stock Dividends and Other Distributions. If the Company at any
time while this Warrant is outstanding and unexpired shall (i) pay a dividend
with respect to Series Preferred payable in Series Preferred, or (ii) make any
other distribution with respect to Series Preferred (except any distribution
specifically provided for in Sections 4(a) and 4(b), of Series Preferred, then
the Warrant Price shall be adjusted, from and after the date of determination of
shareholders entitled to receive such dividend or distribution, to that price
determined by

                                       3.
<PAGE>

multiplying the Warrant Price in effect immediately prior to such date of
determination by a fraction (i) the numerator of which shall be the total number
of shares of Series Preferred outstanding immediately prior to such dividend or
distribution, and (ii) the denominator of which shall be the total number of
shares of Series Preferred outstanding immediately after such dividend or
distribution.

          (d) Adjustment of Number of Shares. Upon each adjustment in the
Warrant Price, the number of Shares of Series Preferred purchasable hereunder
shall be adjusted, to the nearest whole share, to the product obtained by
multiplying the number of Shares purchasable immediately prior to such
adjustment in the Warrant Price by a fraction, the numerator of which shall be
the Warrant Price immediately prior to such adjustment and the denominator of
which shall be the Warrant Price immediately thereafter.

          (e) Antidilution Rights. The other antidilution rights applicable to
the Shares of Series Preferred purchasable hereunder are set forth in the
Company's Certificate of Incorporation, as amended through the Date of Grant, a
true and complete copy of which is attached hereto as Exhibit B (the "Charter").
Such antidilution rights shall not be restated, amended, modified or waived in
any manner that is adverse to the holder hereof without such holder's prior
written consent. The Company shall promptly provide the holder hereof with any
restatement, amendment, modification or waiver of the Charter promptly after the
same has been made.

     5.   Notice of Adjustment.  Whenever the Warrant Price or the number of
Shares purchasable hereunder shall be adjusted pursuant to Section 4 hereof, the
Company shall make a certificate signed by its chief financial officer setting
forth, in reasonable detail, the event requiring the adjustment, the amount of
the adjustment, the method by which such adjustment was calculated, and the
Warrant Price and the number of Shares purchasable hereunder after giving effect
to such adjustment, and shall cause copies of such certificate to be mailed
(without regard to Section 13 hereof, by first class mail, postage prepaid) to
the holder of this Warrant.  In addition, whenever the conversion price or
conversion ratio of the Series Preferred shall be adjusted, the Company shall
make a certificate signed by its chief financial officer setting forth, in
reasonable detail, the event requiring the adjustment, the amount of the
adjustment, the method by which such adjustment was calculated, and the
conversion price or ratio of the Series Preferred after giving effect to such
adjustment, and shall cause copies of such certificate to be mailed (without
regard to Section 13 hereof, by first class mail, postage prepaid) to the holder
of this Warrant.

     6.   Fractional Shares.  No fractional shares of Series Preferred will be
issued in connection with any exercise hereunder, but in lieu of such fractional
shares the Company shall make a cash payment therefor based on the fair market
value of the Series Preferred on the date of exercise as reasonably determined
in good faith by the Company's Board of Directors.

     7.   Compliance with Act: Disposition of Warrant or Shares of Series
Preferred.

          (a) Compliance with Act. The holder of this Warrant, by acceptance
hereof; agrees that this Warrant, and the shares of Series Preferred to be
issued upon exercise hereof and any Common Stock issued upon conversion thereof
are being acquired for investment and that

                                       4.
<PAGE>

such holder will not offer, sell or otherwise dispose of this Warrant, or any
shares of Series Preferred to be issued upon exercise hereof or any Common Stock
issued upon conversion thereof except under circumstances which will not remit
in a violation of the Act or any applicable state securities laws. Upon exercise
of this Warrant, unless the Shares being acquired are registered under the Act
and any applicable state securities laws or an exemption from such registration
is available, the holder hereof shall confirm in writing that the shares of
Series Preferred so purchased (and any shares of Common Stock issued upon
conversion thereof) are being acquired for investment and not with a view toward
distribution or resale in violation of the Act and shall confirm such other
matters related thereto as may be reasonably requested by the Company. This
Warrant and all shares of Series Preferred issued upon exercise of this Warrant
and all shares of Common Stock issued upon conversion thereof (unless registered
under the Act and any applicable state securities laws) shall be stamped or
imprinted with a legend in substantially the following form:

     "THE SECURITIES EVIDENCED HEREBY HAVE NOT BEEN REGISTERED UNDER THE
     SECURITIES ACT OF 1933, AS AMENDED, OR ANY STATE SECURITIES LAWS.
     NO SALE OR DISPOSITION MAY BE EFFECTED WITHOUT (i) EFFECTIVE
     REGISTRATION STATEMENTS RELATED THERETO, (ii) AN OPINION OF COUNSEL
     OR OTHER EVIDENCE REASONABLY SATISFACTORY TO THE COMPANY, THAT SUCH
     REGISTRATIONS ARE NOT REQUIRED, (iii) RECEIPT OF NO-ACTION LETTERS
     FROM THE APPROPRIATE GOVERNMENTAL AUTHORITIES, OR (iv) OTHERWISE
     COMPLYING WITH THE PROVISIONS OF SECTION 7 OF THE WARRANT UNDER
     WHICH THESE SECURITIES WERE ISSUED, DIRECTLY OR INDIRECTLY."

     Said legend shall be removed by the Company, upon the request of a holder,
at such time as the restrictions on the transfer of the applicable security
shall have terminated.  In addition, in connection with the issuance of this
Warrant, the holder specifically represents to the Company by acceptance of this
Warrant as follows:

                    (1) The holder is aware of the Company's business affairs
and financial condition, and has acquired information about the Company
sufficient to reach an informed and knowledgeable decision to acquire this
Warrant. The holder is acquiring this Warrant for its own account for investment
purposes only and not with a view to, or for the resale in connection with, any
"distribution" thereof in violation of the Act.

                    (2) The holder understands that this Warrant has not been
registered under the Act in reliance upon a specific exemption therefrom, which
exemption depends upon, among other things, the bona fide nature of the holder's
investment intent as expressed herein.

                    (3) The holder further understands that this Warrant must be
held indefinitely unless subsequently registered under the Act and qualified
under any applicable state securities laws, or unless exemptions from
registration and qualification are otherwise available. The holder is aware of
the provisions of Rule 144, promulgated under the Act.

                                       5.
<PAGE>

          (b) Disposition of Warrant or Shares. With respect to any offer, sale
or other disposition of this Warrant or any shares of Series Preferred acquired
pursuant to the exercise of this Warrant prior to registration of such Warrant
or shares, the holder hereof agrees to give written notice to the Company prior
thereto, describing briefly the manner thereof, together with a written opinion
of such holder's counsel, or other evidence, if reasonably requested by the
Company, to the effect that such offer, sale or other disposition may be
effected without registration or qualification (under the Act as then in effect
or any federal or state securities law then in effect) of this Warrant or such
shares of Series Preferred or Common Stock and indicating whether or not under
the Act certificates for this Warrant or such shares of Series Preferred to be
sold or otherwise disposed of require any restrictive legend as to applicable
restrictions on transferability in order to ensure compliance with such law.
Promptly upon receiving such written notice and reasonably satisfactory opinion
or other evidence, if so requested, Company, as promptly as practicable but no
later than fifteen (15) days after receipt of the written notice, shall notify
such holder that such holder may sell or otherwise dispose of this Warrant or
such shares of Series Preferred or Common Stock, all in accordance with the
terms of the notice delivered to the Company. If determination has been made
pursuant to this Section 7(b) that the opinion of counsel for the holder or
other evidence is not reasonably satisfactory to the Company, the Company shall
so notify the holder promptly with details thereof after such determination has
been made. Notwithstanding the foregoing, this Warrant or such shares of Series
Preferred or Common Stock may, as to such federal laws, be offered, sold or
otherwise disposed of in accordance with Rule 144 or 144A under the Act,
provided that the Company shall have been furnished with such information as the
Company may reasonably request to provide a reasonable assurance that the
provisions of Rule 144 or 144A have been satisfied. Each certificate
representing this Warrant or the shares of Series Preferred thus transferred
(except a transfer pursuant to Rule 144 or 144A) shall bear a legend as to the
applicable restrictions on transferability in order to ensure compliance with
such laws, unless in the aforesaid opinion of counsel for the holder, such
legend is not required in order to ensure compliance with such laws. The Company
may issue stop transfer instructions to its transfer agent in connection with
such restrictions.

          (c) Applicability of Restriction. Neither any restrictions of any
legend described in this Warrant nor the requirements of Section 7(b) above
shall apply to any transfer of, or grant of a security interest in, this Warrant
(or the Series Preferred or Common Stock obtainable upon exercise thereof) or
any part hereof (i) to a partner of the holder if the holder is a partnership,
(ii) to a partnership of which the holder is a partner, or (iii) to any
affiliate of the holder if the holder is a corporation; however, in any such
transfer, if applicable, the transferee shall on the Company's request agree in
writing to be bound by the terms of this Warrant as if an original signatory
hereto.

     8.   Rights as Shareholders; Information.  No holder of this Warrant, as
such, shall be entitled to vote or receive dividends or be deemed the holder of
Series Preferred or any other securities of the Company which may at any time be
issuable on the exercise hereof for any purpose, nor shall anything contained
herein be construed to confer upon the holder of this Warrant, as such, any of
the rights of a shareholder of the Company or any right to vote for the election
of directors or upon any matter submitted to shareholders at any meeting
thereof, or to receive notice of meetings, or to receive dividends or
subscription rights or otherwise until this Warrant shall have been exercised
and the Shares purchasable upon the exercise hereof shall

                                       6.
<PAGE>

have become deliverable, as provided herein. Notwithstanding the foregoing, the
Company will transmit to the holder of this Warrant such information, documents
and reports as are generally distributed to the holders of any class or series
of the securities of the Company concurrently with the distribution thereof to
the shareholders.

     9.   Registration Rights.  The Company grants registration rights to the
holder of this Warrant for any Common Stock of the Company obtained upon
conversion of the Series Preferred, comparable to the registration rights
granted to the investors in that certain Registration Rights Agreement dated as
of January 27, 1995 (the "Registration Rights Agreement"), with the following
exceptions and clarifications:

                    (1) The holder will have no demand registration rights.

                    (2) The holder will be subject to the same provisions
regarding indemnification as contained in the Registration Rights Agreement.

                    (3) The registration rights are freely assignable by the
holder of this Warrant.

     10.  Additional Rights.

          10.1 Secondary Sales.  The Company agrees that it will not interfere
with the holder of this Warrant in obtaining liquidity if opportunities to make
secondary sales of the Company's securities become available.  To this end, the
Company will promptly provide the holder of this Warrant with notice of any
offer (of which it has knowledge) to acquire from the Company's security holders
more than five percent (5%) of the total voting power of the Company and will
not interfere with any attempt by the holder in arranging the sale of this
Warrant to the person or persons making such offer.

          10.2 Mergers.  The Company shall provide the holder of this Warrant
with at least thirty (30) days' notice of the terms and conditions of any of the
following potential transactions: (i) the sale, lease, exchange, conveyance or
other disposition of all or substantially all of the Company's property or
business, or (ii) its merger into or consolidation with any other corporation
(other than a wholly-owned subsidiary of the Company), or any transaction
(including a merger or other reorganization) or series of related transactions,
in which more than 50% of the voting power of the Company is disposed of.  The
Company will cooperate with the holder in arranging the sale of this Warrant in
connection with any such transaction.

          10.3 Right to Convert Warrant into Stock: Net Issuance.

               (a) Right to Convert. In addition to and without limiting the
rights of the holder under the terms of this Warrant, the holder shall have the
right to convert this Warrant or any portion thereof (the "Conversion Right")
into shares of Series Preferred (or Common Stock if the Series Preferred has
been automatically converted into Common Stock) as provided in this Section 10.3
at any time or from time to time during the term of this Warrant. Upon exercise
of the Conversion Right with respect to a particular number of shares subject to
this Warrant (the "Converted Warrant Shares"), the Company shall deliver to the
holder (without payment by the holder of any exercise price or any cash or other
consideration) (X) that number

                                       7.
<PAGE>

of shares of fully paid and nonassessable Series Preferred (or Common Stock if
the Series Preferred has been automatically converted into Common Stock) equal
to the quotient obtained by dividing the value of this Warrant (or the specified
portion hereof) on the Conversion Date (as defined in subsection (b) hereof),
which value shall be determined by subtracting (A) the aggregate Warrant Price
of the Converted Warrant Shares immediately prior to the exercise of the
Conversion Right from (B) the aggregate fair market value of the Converted
Warrant Shares issuable upon exercise of this Warrant (or the specified portion
hereof) on the Conversion Date (as herein defined) by (Y) the fair market value
of one share of Series Preferred (or Common Stock if the Series Preferred has
been automatically converted into Common Stock) on the Conversion Date (as
herein defined).

     Expressed as a formula, such conversion (assuming the Series Preferred has
been automatically converted into Common Stock) shall be computed as follows:

                                   X = B - A
                                       _____
                                         Y

Where:    X =  The number of shares of Common Stock that may be issued to
               holder.

          Y =  The fair market value (FMV) of one share of Common Stock.

          A =  The aggregate Warrant Price (i.e., Converted Warrant Shares x
               Warrant Price).

          B =  The aggregate FMV (i.e., FMV x Converted Warrant Shares).

     No fractional shares shall be issuable upon exercise of the Conversion
Right, and, if the number of shares to be issued determined in accordance with
the foregoing formula is other than a whole number, the Company shall pay to the
holder an amount in cash equal to the fair market value of the resulting
fractional share on the Conversion Date (as hereinafter defined).  For purposes
of Section 9 of this Warrant, shares issued pursuant to the Conversion Right
shall be treated as if they were issued upon the exercise of this Warrant.

          (b) Method of Exercise.  The Conversion Right may be exercised by the
holder by the surrender of this Warrant at the principal office of the Company
together with a written statement specifying that the holder thereby intends to
exercise the Conversion Right and indicating the number of shares subject to
this Warrant which are being surrendered (referred to in Section 10.3(a) hereof
as the Converted Warrant Shares) in exercise of the Conversion Right Such
conversion shall be effective upon receipt by the Company of this Warrant
together with the aforesaid written statement, or on such later date as is
specified therein (the "Conversion Date"), and, at the election of the holder
hereof, may be made contingent upon the closing of the sale of the Company's
Common Stock to the public in a public offering pursuant to a Registration
Statement under the Act (a "Public Offering").  Certificates for the shares
issuable upon exercise of the Conversion Right and, if applicable, a new warrant
evidencing the balance of the shares remaining subject to this Warrant shall be
issued as of the Conversion Date and shall be delivered to the holder within
thirty (30) days following the Conversion Date.  Any conversion from Series
Preferred to Common Stock shall be in the ratio of one (1) share of Common Stock
for each share of Series Preferred (as adjusted hereto and in the Charter).  On
the

                                       8.
<PAGE>

Date of Grant, each share of the Series Preferred represented by this Warrant is
convertible into one share of Common Stock.

          (c) Determination of Fair Market Value. For purposes of this Section
10.3, "fair market value" of a share of Series Preferred (or Common Stock if the
Series Preferred has been automatically convened into Common Stock) as of a
particular date (the "Determination Date") shall mean:

              (i)  If the Conversion Right is exercised in connection with and
contingent upon a Public Offering, and if the Company's Registration Statement
relating to such Public Offering ("Registration Statement") has been declared
effective by the SEC, then the initial "Price to Public" specified in the final
prospectus with respect to such offering.

              (ii) If the Conversion Right is not exercised in connection with
and contingent upon a Public Offering, then as follows:

                   (1) If traded on a securities exchange, the fair market value
of the Common Stock shall be deemed to be the average of the closing prices of
the Common Stock on such exchange over the 30-day period ending five business
days prior to the Determination Date, and the fair market value of the Series
Preferred shall be deemed to be such fair market value of the Common Stock
multiplied by the number of shares of Common Stock into which each share of
Series Preferred is then convertible;

                   (2) If traded over-the-counter, the fair market value of the
Common Stock shall be deemed to be the average of the closing bid prices of the
Common Stock over the 30-day period ending five business days prior to the
Determination Date, and the fair market value of the Series Preferred shall be
deemed to be such fair market value of the Common Stock multiplied by the number
of shares of Common Stock into which each share of Series Preferred is then
convertible; and

                   (3) If there is no public market for the Common Stock, then
fair market value shall be determined by mutual agreement of the holder of this
Warrant and the Company.

     11.  Representations and Warranties.  The Company represents and warrants
to the holder of this Warrant as follows:

          (a) This Warrant has been duly authorized and executed by the Company
and is a valid and binding obligation of the Company enforceable in accordance
with its terms, subject to laws of general application relating to bankruptcy,
insolvency and the relief of debtors and the rules of law or principles at
equity governing specific performance, injunctive relief and other equitable
remedies;

          (b) The Shares have been duly authorized and reserved for issuance: by
the Company and, when issued in accordance with the terms hereof, will be
validly issued, fully paid and non-assessable;

                                       9.
<PAGE>

          (c) The rights, preferences, privileges and restrictions granted to or
imposed upon the Series Preferred and the holders thereof are as set forth in
the Charter, as amended to the Date of the Grant, a true and complete copy of
which has been delivered to the original holder of this Warrant and is attached
hereto as Exhibit B;

          (d) The shares of Common Stock issuable upon conversion of the Shares
have been duly authorized and reserved for issuance by the Company and, when
issued in accordance with the terms of the Charter will be validly issued, fully
paid and nonassessable;

          (e) The execution and delivery of this Warrant are not, and the
issuance of the Shares upon exercise of this Warrant in accordance with the
terms hereof will not be, inconsistent with the Company's Charter or by-laws, do
not and will not contravene any law, governmental rule or regulation, judgment
or order applicable to the Company, and do not and will not conflict with or
contravene any provision of, or constitute a default under, any indenture,
mortgage, contact or other instrument of which the Company is a party or by
which it is bound or require the consent or approval of, the giving of notice
to, the registration or filing with or the taking of any action in respect of or
by, any Federal, state or local government authority or agency or other person,
except for the filing of notices pursuant to federal and state securities laws,
which filings will be effected by the time required thereby; and

          (f) There are no actions, suits, audits, investigations or proceedings
pending or, to the knowledge of the Company, threatened against the Company in
any court or before any governmental commission, board or authority which, if
adversely determined, will have a material adverse effect on the ability of the
Company to perform its obligations under this Warrant.

     12.  Modification and Waiver.  This Warrant and any provision hereof may be
changed, waived, discharged or terminated only by an instrument in writing
signed by the party against which enforcement of the same is sought

     13.  Notices. Any notice, request, communication or other document required
or permitted to be given or delivered to the holder hereof or the Company shall
be delivered, or shall be sent by certified or registered mail, postage prepaid,
to each such holder at its address as shown on the books of the Company or to
the Company at the address indicated therefor on the signature page of this
Warrant.

     14.  Binding Effect on Successors.  This Warrant shall be binding upon any
corporation succeeding the Company by merger, consolidation or acquisition of
all or substantially all of the Company's assets, and all of the obligations of
the Company relating to the Series Preferred issuable upon the exercise or
conversion of this Warrant shall survive the exercise, conversion and
termination of this Warrant and all of the covenants and agreements of the
Company shall inure to the benefit of the successors and assigns of the holder
hereof.  The Company will, at the time of the exercise or conversion of this
Warrant, in whole or in part, upon request of the holder hereof but at the
Company's expense, acknowledge in writing its continuing obligation to the
holder hereof in respect of any rights (including, without limitation, any right
to registration of the Shares) to which the holder hereof shall continue to be
entitled after such exercise or conversion in accordance with this Warrant;
provided, that the failure of

                                      10.
<PAGE>

the holder hereof to make any such request shall not affect the continuing
obligation of the Company to the holder hereof in respect of such rights.

     15.  Lost Warrants or Stock Certificates.  The Company covenants to the
holder hereof that, upon receipt of evidence reasonably satisfactory to the
Company of the loss, theft, destruction or mutilation of this Warrant or any
stock certificate and, in this case of any such loss, theft or destruction, upon
receipt of an indemnity reasonably satisfactory to the Company, or in the case
of any such mutilation upon surrender and cancellation of such Warrant or stock
certificate, the Company will make and deliver a new Warrant or stock
certificate, of like tenor, in lieu of the lost, stolen, destroyed or mutilated
Warrant or stock certificate.

     16.  Descriptive Headings. The descriptive headings of the several
paragraphs of this Warrant are inserted for convenience only and do not
constitute a part of this Warrant. The language in this Warrant shall be
constructed as to its fair meaning without regard to which party drafted this
Warrant.

     17.  Governing Law.  This Warrant shall be construed and enforced in
accordance with, and the rights of the parties shall be governed by, the laws of
the State of California; provided, however, that any matters herein dealing with
the internal corporate governance of the Company or the rights, preferences and
privileges applicable to the Company's capital stock shall be governed by the
laws of the State of Delaware.

     18.  Survival of Representations, Warranties and Agreements.  All
representations and warranties of the Company and the holder hereof contained
herein shall survive the Date of Grant, the exercise or conversion of this
Warrant (or any part hereof) or the termination or expiration of rights
hereunder.  All agreements of the Company and the holder hereof contained herein
shall survive indefinitely until, by respective terms, they are no longer
operative.

     19.  Remedies.  In case any one or more of the covenants and agreements
contained in this Warrant shall have been breached, the holders hereof (in the
case of a breach by the Company), or the Company (in the case of a breach by a
holder), may proceed to protect and enforce their or its rights either by suit
in equity and/or by action at law, including, but not limited to, an action for
damages as a result of any such breach and/or an action for specific performance
of any such covenant or agreement contained in this Warrant.

     20.  No Impairment of Rights.  The Company will not, by amendment of its
Charter or through any other means, 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
action as may be necessary or appropriate in order to protect the rights of the
holder of this Warrant against impairment.

     21.  Severability.  The invalidity or unenforceability of any provision of
this Warrant in any jurisdiction shall not affect tile validity or
enforceability of such provision in any other jurisdiction, or affect any other
provision of this Warrant, which shall remain in full force and effect.

     22.  Recovery of Litigation Costs.  If any legal action or other proceeding
is brought for the enforcement of this Warrant, or because of an alleged
dispute, breach, default, or

                                      11.
<PAGE>

misrepresentation in connection with any of the provisions of this Warrant, the
successful or prevailing party or parties shall be entitled to recover
reasonable attorneys' fees and other costs incurred in that action or
proceeding, in addition to any other relief to which it or they may be entitled.

     23.  Entire Agreement: Modification.  This Warrant constitutes the entire
agreement between the parties pertaining to the subject matter contained in it
and supersedes all prior and contemporaneous agreements, representations, and
undertakings of the parties, whether oral or written, with respect to such
subject matter.

Date of Grant:  January 24, 1996   EXELIXIS PHARMACEUTICALS, INC.,
                                   a Delaware corporation

                                   By: /s/ Jean-Francois Formela
                                      ------------------------------------------

                                   Name: Jean-Francois Formela
                                        ----------------------------------------

                                   Title: Chief Executive Officer
                                         ---------------------------------------
                                   Address:  One Kendall Square Building 600
                                             Cambridge, MA 02139

                                      12.
<PAGE>

                                   EXHIBIT A

                              NOTICE OF EXERCISE

To:  EXELIXIS PHARMACEUTICALS, INC

     1.   The undersigned hereby:

          [_]  elects to purchase _________ shares of _________ Stock of
               EXELIXIS PHARMACEUTICALS, INC. pursuant to the terms of the
               attached Warrant, and tenders herewith payment of the purchase
               price of such shares in full, or

          [_]  elects to exercise its net issuance rights pursuant to Section
               10.3 of the attached Warrant with respect to ___________ Shares
               of __________Stock.

     2.   Please issue a certificate or certificates representing said shares in
the name of the undersigned or in such other name or names as are specified
below:

               _____________________________________
                              (Name)

               _____________________________________

               _____________________________________
                             (Address)

     3.   The undersigned represents that the aforesaid shares are being
acquired for the account of the undersigned for investment and not with a view
to, or for resale in connection with, the distribution thereof and that the
undersigned has no present intention of distributing or reselling such shares,
all except as in compliance with applicable securities laws.

__________________
Date

                                             ___________________________________
                                             Signature

                                      13.
<PAGE>

                                  EXHIBIT A-I

                              NOTICE OF EXERCISE

To:  EXELIXIS PHARMACEUTICALS. INC. (the "Company")

     1.   Contingent upon and effective immediately prior to the closing (the
"Closing") of the Company's public offering contemplated by the Registration
Statement on Form S____ , filed ________, 19___, the undersigned hereby:

          [_]  elects to purchase ______ shares of ______ Stock of the Company
               (or such lesser number of shares as may be sold on behalf of the
               undersigned at the Closing) pursuant to the terms of the attached
               Warrant, or

          [_]  elects to exercise its net issuance rights pursuant to Section
               10.3 of the attached Warrant with respect to Shares of Stock.

     2.   Please deliver to the custodian for the selling shareholders a stock
certificate representing such __________ shares.

     3.   The undersigned has instructed the custodian for the selling
shareholders to deliver to the Company $__________ or, if less, the net proceeds
due the undersigned from the sale of shares in the aforesaid public offering. If
such net proceeds are less than the purchase price for such shares, the
undersigned agrees to deliver the difference to the Company prior to the
Closing.

_________________
Date

                                             ___________________________________
                                             Signature

                                      14.<PAGE>

                                                                     EXHIBIT 4.6

          THIS WARRANT HAS NOT BEEN REGISTERED UNDER THE SECURITIES
          ACT OF 1933, AS AMENDED, OR ANY STATE SECURITIES LAWS. NO
          SALE OR DISPOSITION MAY BE EFFECTED) WITHOUT (i) EFFECTIVE
          REGISTRATION STATEMENTS RELATED THERETO, (ii) AN OPINION OF
          COUNSEL OR OTHER EVIDENCE, REASONABLY SATISFACTORY TO THE
          COMPANY, THAT SUCH REGISTRATIONS ARE NOT REQUIRED, (iii)
          RECEIPT OF NO-ACTION LETTERS FROM THE APPROPRIATE
          GOVERNMENTAL AUTHORITIES, OR (IV) OTHERWISE COMPLYING WITH
          THE PROVISIONS OF SECTION 7 OF THIS WARRANT.

                        EXELIXIS PHARMACEUTICALS, INC.

                       WARRANT TO PURCHASE 85,000 SHARES

                                OF COMMON STOCK

     This Certifies That, for value received, MMC/GATX Partnership No. 1 and its
assignees are entitled to subscribe for and purchase 85,000 shares of the fully
paid and nonassessable Common Stock (as adjusted pursuant to Section 4 hereof,
the "Shares") of Exelixis Pharmaceuticals, Inc., a Delaware corporation (the
"Company"), at the price of $2.00 per share (such price and such other price as
shall result, from time to time, from the adjustments specified in Section 4
hereof is hereto referred to as the "Warrant Price"), subject to the provisions
and upon the terms and conditions hereinafter set forth. As used herein, (a) the
term "Date of Grant" shall mean September 25, 1997, and (b) the term "Other
Warrants" shall mean any other warrants issued by the Company in connection with
the instruction with respect to which this Warrant was issued, and any warrant
issued upon transfer or partial exercise of this Warrant. The term "Warrant" as
used herein shall be deemed to include Other Warrants unless the context clearly
requires otherwise.

1.   Term.  The purchase right represented by this Warrant is exercisable, in
whole or in part, at any time and from time to time from the Date of Grant
through the later of (i) ten (10) years after the Date of Grant or (ii) five (5)
years after the closing of the Company's initial public offering of its Common
Stock effected pursuant to a Registration Statement on Form S-I (or its
successor) filed under the Securities Act of 1933, as amended (the "Act").

2.   Method of Exercise: Payment: Issuance of New Warrant.  Subject to Section I
hereof, the purchase right represented by this Warrant may be exercised by the
holder hereof, in whole or in part and from time to time, at the election of the
holder hereof, by (a) the surrender of this Warrant (with the notice of exercise
substantially in the form attached hereto as Exhibit A duly completed and
executed) at the principal office of the Company and by the payment to the
Company, by certified or bank check, or by wire transfer to an account
designated by the Company (a "Wire Transfer") of an amount equal to the then
applicable Warrant Price multiplied by the number of Shares then being
purchased, or (b) if in connection with a registered public offering of the
Company's securities, the surrender of this Warrant (with the notice of exercise
form attached hereto as Exhibit A- 1 duly completed and executed) at the
principal office of the Company together with notice of arrangements reasonably
satisfactory to the Company for payment to the Company either by certified or
bank check or by Wire Transfer from the proceeds

                                       1.
<PAGE>

of the sale of shares to be sold by the holder in such public offering of an
amount equal to the then applicable Warrant Price per share multiplied by the
number of Shares then being purchased, or (c) exercise of the right provided for
in Section 10.3 hereof. The person or persons in whose name(s) any
certificate's) representing the Shares shall be issuable upon exercise of this
Warrant shall be deemed to have become the holder(s) of record of, and shall be
treated for all purposes as the record holder(s) of, the shares represented
thereby (and such shares shall be deemed to have been issued) immediately prior
to the close of business on the date or dates upon which this Warrant is
exercised. In the event of any exercise of the rights represented by this
Warrant, certificates for the shares of stock so purchased shall be delivered to
the holder hereof as soon as possible and in any event within thirty (30) days
after such exercise and, unless this Warrant has been exercised or expired, a
new Warrant representing the portion of the Shares, if any, with respect to
which this Warrant shall not then have been exercised shall also be issued to
the holder hereof as soon as possible and in any event within such thirty-day
period.

3.   Stock Fully Paid: Reservation of Shares.  All Shares that may be issued
upon the exercise of the rights represented by this Warrant will, upon issuance
pursuant to the terms and conditions herein, be fully paid and nonassessable,
and free from all taxes, liens and charges with respect to the issue thereof.
During the period within which the rights represented by this Warrant may be
exercised, the Company will at all times have authorized, and reserved for the
purpose of the issue upon exercise of the purchase rights evidenced by this
Warrant, a sufficient number of shares of its Common Stock to provide for the
exercise of the rights represented by this Warrant.

4.   Adjustment of Warrant Price and Number of Shares.  The number and kind of
securities purchasable upon the exercise of this Warrant and the Warrant Price
shall be subject to adjustment from time to time upon the occurrence of certain
events, as follows:

     (a)  Reclassification or Merger.  In case of any reclassification or change
of securities of the class issuable upon exercise of this Warrant (other than a
change in par value, or from par value to no par value, or from no par value to
par value, or as a result of a subdivision or combination), or in case of any
merger of the Company with or into another corporation (other than a merger with
another corporation in which the Company is the acquiring and the surviving
corporation and which does not result in any reclassification or change of
outstanding securities issuable upon exercise of this Warrant), or in case of
any sale of all or substantially all of the assets of the Company, the Company,
or such successor or purchasing corporation, as the case may be, shall duly
execute and deliver to the holder of this Warrant a new Warrant (in form and
substance satisfactory to the holder of this Warrant), so that the holder of
this Warrant shall have the right to receive, at a total purchase price not to
exceed that payable upon the exercise of the unexercised portion of this
Warrant, and in lieu of the shares of Common Stock theretofore issuable upon
exercise of this Warrant, the kind and amount of shares of stock, other
securities, money and property receivable upon such reclassification, change or
merger by a holder of the number of shares of Common Stock then purchasable
under this Warrant.  Such new Warrant shall provide for adjustments that shall
be as nearly equivalent as may be practicable to the adjustments provided for in
this Section 4.  The provisions of this subparagraph (a) shall similarly apply
to successive reclassifications, changes, mergers and transfers.

                                       2.
<PAGE>

     (b)  Subdivision or Combination of Shares. If the Company at any time
while this Warrant remains outstanding and unexpired shall subdivide or
combine its outstanding shares of Common Stock, the Warrant Price shall be
proportionately decreased in the case of a subdivision or increased in the
case of a combination, effective at the close of business on the date the
subdivision or combination becomes effective.

     (c)  Stock Dividends and Other Distribution.  If the Company at any time
while this Warrant is outstanding and unexpired shall (i) pay a dividend with
respect to Common Stock payable in Common Stock, or (ii) make any other
distribution of Common Stock with respect to Common Stock (except any
distribution specifically provided for in Sections 4(a) and 4(b)), then the
Warrant Price shall be adjusted, from and after the date of determination of
shareholders entitled to receive such dividend or distribution, to that price
determined by multiplying the Warrant Price in effect immediately prior to such
date of determination by a fraction (i) the numerator of which shall be the
total number of shares of Common Stock outstanding immediately prior to such
dividend or distribution, and (ii) the denominator of which shall be the total
number of shares of Common Stock outstanding immediately after such dividend or
distribution.

     (d)  Adjustment of Number of Shares.  Upon each adjustment in the Warrant
Price, the number of Shares purchasable hereunder shall be adjusted, to the
nearest whole share, to the product obtained by multiplying the number of Shares
purchasable immediately prior to such adjustment in the Warrant Price by a
fraction, the numerator of which shall be the Warrant Price immediately prior to
such adjustment and the denominator of which shall be the Warrant Price
immediately thereafter.

     (e)  Antidilution Rights. In the event that the "Series C Conversion Price"
(as defined in the Company's Restated Certificate of Incorporation, as amended
through the Date of Grant, a true and complete copy of which is attached hereto
as Exhibit B (the "Charter")), is reduced from time to time after the Date of
Grant pursuant to the antidilution rights applicable to the Series C Convertible
Preferred Stock set forth in Section 2(f) of Article Fourth of the Charter
(other than reductions covered by Sections 4(b) or 4(c) of this Warrant), then
the same reduction shall be made forthwith to the Warrant Price, subject to
proportionate adjustment to reflect any stock split or combination, stock
dividend or similar event occurring after the Date of Grant. The intent of this
Paragraph 4(e) is to provide the holder of this Warrant with the same
antidilution protection as would have prevailed if this Warrant had entitled the
holder hereof to purchase shares of the Company's Series C Convertible Preferred
Stock (rather than Common Stock), as such antidilution protection is set forth
in the Charter. Such antidilution rights shall not be amended, modified or
waived in any manner that is materially adverse to the holder hereof without
such holder's prior written consent, which consent shall not be unreasonably
withheld or delayed. The Company shall provide the holder hereof with a copy of
any restatement, amendment, modification or waiver of the Charter promptly after
the same has been made.

5.   Notice of Adjustments.  Whenever the Warrant Price or the number of Shares
purchasable hereunder shall be adjusted pursuant to Section 4 hereof, the
Company shall make a certificate signed by its chief financial officer setting
forth, in reasonable detail, the event requiring the adjustment, the amount of
the adjustment, the method by which such adjustment was calculated, and the
Warrant Price and the number of Shares purchasable hereunder after

                                       3.
<PAGE>

giving effect to such adjustment, and shall cause copies of such certificate to
be mailed (without regard to Section 13 hereof, by first class mall, postage
prepaid) to the holder of this Warrant at such holder's last known address.

6.   Fractional Shares.  No fractional shares of Common Stock will be issued in
connection with any exercise hereunder, but in lieu of such fractional shares
the Company shall make a cash payment therefor based on the fair market value of
the Common Stock on the date of exercise as reasonably determined in good faith
by the Company's Board of Directors.

7.   Compliance with Act: Disposition of Warrant or Shares of Common Stock.

          (a)  Compliance with Act. The holder of this Warrant, by acceptance
hereof, agrees that this Warrant, and the Shares to be issued upon exercise
hereof are being acquired for investment and that such holder will not offer,
sell or otherwise dispose of this Warrant, or any Shares except under
circumstances which will not result in a violation of the Act or any applicable
state securities laws. Upon exercise of this Warrant, unless the Shares being
acquired are registered under the Act and any applicable state securities laws
or an exemption from such registration is available, the holder hereof shall
confirm in writing that the Shares so purchased are being acquired for
investment and not with a view toward distribution or resale in violation of the
Act and shall confirm such other matters related thereto as may be reasonably
requested by the Company. This Warrant and all Shares issued upon exercise of
this Warrant (unless registered under the Act and any applicable state
securities laws) shall be stamped or imprinted with a legend in substantially
the following form:

          "THE SECURITIES EVIDENCED HEREBY HAVE NOT BEEN REGISTERED UNDER
     THE SECURITIES ACT OF 1933, AS AMENDED, OR ANY STATE SECURITIES LAWS.
     NO SALE OR DISPOSITION MAY BE EFFECTED WITHOUT (i) EFFECTIVE
     REGISTRATION STATEMENTS RELATED THERETO, (ii) AN OPINION OF COUNSEL OR
     OTHER EVIDENCE, REASONABLY SATISFACTORY TO THE COMPANY, THAT SUCH
     REGISTRATIONS ARE NOT REQUIRED, (iii) RECEIPT OF NO-ACTION LETTERS
     FROM THE APPROPRIATE GOVERNMENTAL AUTHORITIES, OR (iv) OTHERWISE
     COMPLYING WITH THE PROVISIONS OF SECTION 7 OF THE WARRANT UNDER WHICH
     THESE SECURITIES WERE ISSUED, DIRECTLY OR INDIRECTLY."

     Said legend shall be removed by the Company, upon the request of a holder,
at such time as the restrictions on the transfer of the applicable security
shall have terminated.  In addition, in connection with the issuance of this
Warrant, the holder specifically represents to the Company by acceptance of this
Warrant as follows:

        (i)   The holder is aware of the Company's business affairs and
financial condition, and has acquired information about the Company
sufficient to reach an informed and knowledgeable decision to acquire this
Warrant. The holder is acquiring this Warrant for its own account for
investment purposes only and not with a view to, or for the resale in
connection with, any "distribution" thereof in violation of the Act.

                                       4.
<PAGE>

          (ii)   The holder understands that this Warrant has not been
registered under the Act in reliance upon a specific exemption therefrom,
which exemption depends upon, among other things, the bona fide nature of
the holder's investment intent as expressed herein.

          (iii)  The holder further understands that this Warrant must be
held indefinitely unless subsequently registered under the Act and qualified
under any applicable state securities laws, or unless exemptions from
registration and qualification are otherwise available.  The holder is aware of
the provisions of Rule 144, promulgated under the Act.

     (b)  Disposition of Warrant or Shares.  With respect to any offer, sale or
other disposition of this Warrant or any Shares acquired pursuant to the
exercise of this Warrant prior to registration of such Warrant or Shares, the
holder hereof agrees to give written notice to the Company prior thereto,
describing briefly the manner thereof, together with a written opinion of such
holder's counsel, or other evidence, if reasonably requested by the Company, to
the effect that such offer, sale or other disposition may be effected without
registration or qualification (under the Act as then in effect or any federal or
state securities law then in effect) of this Warrant or the Shares and
indicating whether or not under the Act certificates for this Warrant or the
Shares to be sold or otherwise disposed of require any restrictive legend as to
applicable restrictions on transferability in order to ensure compliance with
such law.  Promptly upon receiving such written notice and reasonably
satisfactory opinion or other evidence, if so requested, the Company, as
promptly as practicable but no later than fifteen (15) days after receipt of the
written notice, shall notify such holder that such holder may sell or otherwise
dispose of this Warrant or such Shares, all in accordance with the terms of the
notice delivered to the Company.  If a determination has been made pursuant to
this Section 7(b) that the opinion of counsel for the holder or other evidence
is not reasonably satisfactory to the Company, the Company shall so notify the
holder promptly with details thereof after such determination has been made.
Notwithstanding the foregoing, this Warrant or such Shares may, as to such
federal laws, be offered, sold or otherwise disposed of in accordance with Rule
144 or 144A under the Act, provided that the Company shall have been furnished
with such information as the Company may reasonably request to provide a
reasonable assurance that the provisions of Rule 144 or 144A have been
satisfied.  Each certificate representing this Warrant or the Shares thus
transferred (except a transfer pursuant to Rule 144 or 144A) shall bear a legend
as to the applicable restrictions on transferability in order to ensure
compliance with such laws, unless in the aforesaid opinion of counsel for the
holder, such legend is not required in order to ensure compliance with such
laws.  The Company may issue stop transfer instructions to its transfer agent in
connection with such restrictions.

     (c)  Applicability of Restrictions.  Neither any restrictions of any legend
described in this Warrant nor the requirements of Section 7(b) above shall
apply to any transfer of, or grant of a security interest in, this Warrant (or
the Common Stock obtainable upon exercise thereof) or any part hereof (i) to a
partner of the holder if the holder is a partnership, (ii) to a partnership of
which the holder is a partner, or (iii) to any affiliate of the holder if the
holder is a corporation; provided, however, in any such transfer, if applicable,
the transferee shall on the Company's request agree in writing to be bound by
the terms of this Warrant as if an original signatory hereto.

                                       5.
<PAGE>

8.   Rights as Shareholders: Information.  No holder of this Warrant, as such,
shall be entitled to vote or receive dividends or be deemed the holder of
Shares, nor shall anything contained herein be construed to confer upon the
holder of this Warrant, as such, any of the rights of a shareholder of the
Company or any right to vote for the election of directors or upon any matter
submitted to shareholders at any meeting thereof, or to receive notice of
meetings, or to receive dividends or subscription rights or otherwise until this
Warrant shall have been exercised and the Shares purchasable upon the exercise
hereof shall have become deliverable, as provided herein.  Notwithstanding the
foregoing, the Company will transmit to the holder of this Warrant such
information, documents and reports as are generally distributed to the holders
of any class or series of the securities of the Company concurrently with the
distribution thereof to the shareholders.

9.   Registration Rights.  The Company grants registration rights to the holder
of this Warrant for any Common Stock of the Company obtained upon exercise
hereof, comparable to the registration rights granted in that certain Second
Amended and Restated Registration Rights Agreement dated as of April 8, 1997
(the "Registration Rights Agreement") to the Investors (as defined in the
Registration Rights Agreement), with the following exceptions:

          (i)   The holder will have no demand registration rights.

          (ii)  The holder will be subject to the same provisions regarding
indemnification as contained in the Registration Rights Agreement.

          (iii) The registration rights are freely assignable by the holder
of this Warrant.

10.  Additional Rights.

     10.1 Secondary Sales.  The Company agrees that it will not interfere with
the holder of this Warrant in obtaining liquidity if opportunities to make
secondary sales of the Company's securities become available.  To this end, the
Company will promptly provide the holder of this Warrant with notice of any
offer (of which it has knowledge) to acquire from the Company's security holders
more than five percent (5%) of the total voting power of the Company and will
not interfere with any attempt by the holder in arranging the sale of this
Warrant to the person or persons making such offer.

     10.2 Mergers.  The Company shall provide the holder of this Warrant with at
least thirty (30) days' notice of the terms and conditions of any of the
following potential transactions: (i) the sale, lease, exchange, conveyance or
other disposition of all or substantially all of the Company's property or
business, or (ii) its merger into or consolidation with any other corporation
(other than a wholly-owned subsidiary of the Company), or any transaction
(including a merger or other reorganization) or series of related transactions,
in which more than 50 % of the voting power of the Company is disposed of.  The
Company will cooperate with the holder in arranging the sale of this Warrant in
connection with any such transaction.

                                       6.
<PAGE>

     10.3 Right to Convert Warrant into Stock: Net Issuance.

          (a)  Right to Convert. In addition to and without limiting the
rights of the holder under the terms of this Warrant, the holder shall have
the right to convert this Warrant or any portion thereof (the "Conversion
Right") into shares of Common Stock as provided in this Section 10.3 at any
time or from time to time during the term of this Warrant. Upon exercise of
the Conversion Right with respect to a particular number of shares subject
to this Warrant (the "Convened Warrant Shares"), the Company shall deliver
to the holder (without payment by the holder of any exercise price or any
cash or other consideration) (X) that number of shares of fully paid and
nonassessable Common Stock equal to the quotient obtained by dividing the
value of this Warrant (or the specified portion hereof on the Conversion
Date (as defined in subsection (b) hereof), which value shall be determined
by subtracting (A) the aggregate Warrant Price of the Converted Warrant
Shares immediately prior to the exercise of the Conversion Right from (B)
the aggregate fair market value of the Convened Warrant Shares issuable
upon exercise of this Warrant (or the specified portion hereof) on the
Conversion Date (as herein defined) by (Y) the fair market value of one
share of Common Stock on the Conversion Date (as herein defined).

     Expressed as a formula, such conversion shall be computed as follows:

     X =  B-A
         ____
           Y

     Where:    X = the number of shares of Common Stock that may be issued to
holder

               Y = the fair market value (FMV) of one share of Common Stock

               A = the aggregate Warrant Price (i.e. Converted Warrant
                   Shares x Warrant Price)

               B = the aggregate FMV (i.e., FMV x Converted Warrant Shares)

     No fractional shares shall be issuable upon exercise of the Conversion
Right, and, if the number of shares to be issued determined in accordance with
the foregoing formula is other than a whole number, the Company shall pay to the
holder an amount in cash equal to the fair market value of the resulting
fractional share on the Conversion Date (as hereinafter defined).  For purposes
of Section 9 of this Warrant, shares issued pursuant to the Conversion Right
shall be treated as if they were issued upon the conversion of this Warrant.

          (b)  Method of Exercise.  The Conversion Right may be exercised by the
holder by the surrender of this Warrant at the principal office of the Company
together with a written statement specifying that the holder thereby intends to
exercise the Conversion Right and indicating the number of shares subject to
this Warrant which are being surrendered (referred to in Section 10.3(a) hereof
as the Converted Warrant Shares) in exercise of the Conversion Right.  Such
conversion shall be effective upon receipt by the Company of this Warrant
together with the aforesaid written statement, or on such later date as is
specified therein (the "Conversion Date"), and, at the election of the holder
hereof, may be made contingent upon the closing of the sale of the Company's
Common Stock to the public in a public offering pursuant to a Registration
Statement under the Act (a "Public Offering").  Certificates for the shares
issuable

                                       7.
<PAGE>

upon exercise of the Conversion Right and, if applicable, a new warrant
evidencing the balance of the shares remaining subject to this Warrant, shall be
issued as of the Conversion Date and shall be delivered to the holder within
thirty (30) days following the Conversion Date.

     (c)  Determination of Fair Market Value. For purposes of this Section
10.3, "fair market value" of a share of Common Stock as of a particular
date (the "Determination Date") shall mean:

          (i)  If the Conversion Right is exercised in connection with and
contingent upon a Public Offering, and if the Company's Registration Statement
relating to such Public Offering ("Registration Statement") has been declared
effective by the SEC, then the initial "Price to Public" specified in the final
prospectus with respect to such offering.

          (ii) If the Conversion Right is not exercised in connection with and
contingent upon a Public Offering, then as follows:

               (A)  If traded on a securities exchange, the fair market
value of the Common Stock shall be deemed to be the average of the closing
prices of the Common Stock on such exchange over the 30-day period ending
five business days prior to the Determination Date;

               (B)  If traded over-the-counter, the fair market value of
the Common Stock shall be deemed to be the average of the closing bid
prices of the Common Stock over the 30-day period ending five business days
prior to the Determination Date; and

               (C)  If there is no public market for the Common Stock, then fair
market value shall be determined by mutual agreement of the holder of this
Warrant and the Company.

11.  Representations and Warranties.  The Company represents and warrants to the
holder of this Warrant as follows:

          (a)  This Warrant has been duly authorized and executed by the
Company and is a valid and binding obligation of the Company enforceable in
accordance with its terms, subject to laws of general application relating
to bankruptcy, insolvency and the relief of debtors and the rules of law or
principles at equity governing specific performance, injunctive relief and
other equitable remedies;

          (b)  The Shares have been duly authorized and reserved for
issuance by the Company and, when issued in accordance with the terms
hereof will be validly issued, fully paid and non-assessable;

          (c)  The rights, preferences, privileges and restrictions granted
to or imposed upon the classes and series of the Company's capital stock
and the holders thereof are as set forth in the Charter and the Second
Amended and Restated Securityholders' Agreement, dated as of April 8, 1997,
among the Company and the Shareholders (as defined therein);

                                       8.
<PAGE>

          (d)  The execution and delivery of this Warrant are not, and the
issuance of the Shares upon exercise of this Warrant in accordance with
the terms hereof will not be, inconsistent with the Company's Charter or by-
laws, do not and will not contravene any law, governmental role or
regulation, judgment or order applicable to the Company, and do not and
will not conflict with or contravene any provision of, or constitute a
default under, any indenture, mortgage, contract or other instrument of
which the Company is a party or by which it is bound or require the consent
or approval of, the giving of notice to, the registration or filing with or
the taking of any action in respect of or by, any Federal, state or local
government authority or agency or other person, except for the filing of
notices pursuant to federal and state securities laws, which filings will
be effected by the time required thereby; and

          (e)  There are no actions, suits, audits, investigations or
proceedings pending or, to the knowledge of the Company, threatened against
the Company in any court or before any governmental commission, board or
authority which, if adversely determined, will have a material adverse
effect on the ability of the Company to perform its obligations under this
Warrant.

12.  Modification and Waiver.  This Warrant and any provision hereof may be
changed, waived, discharged or terminated only by an instrument in writing
signed by the party against which enforcement of the same is sought.

13.  Notices.  Any notice, request, communication or other document required or
permitted to be given or delivered to the holder hereof or the Company shall be
delivered, or shall be sent by certified or registered mail, postage prepaid, to
each such holder at its address as shown on the books of the Company or to the
Company at the address indicated therefor on the signature page of this Warrant.

14.  Binding Effect on Successors.  This Warrant shall be binding upon any
corporation succeeding the Company by merger, consolidation or acquisition of
all or substantially all of the Company's assets, and all of the obligations of
the Company relating to the Shares issuable upon the exercise or conversion of
this Warrant shall survive the exercise, conversion and termination of this
Warrant and all of the covenants and agreements of the Company shall inure to
the benefit of the successors and assigns of the holder hereof.  The Company
will, at the time of the exercise or conversion of this Warrant, in whole or in
part, upon request of the holder hereof but at the Company's expense,
acknowledge in writing its continuing obligation to the holder hereof in respect
of any rights (including, without limitation, any right to registration of the
Shares) to which the holder hereof shall continue to be entitled after such
exercise or conversion in accordance with this Warrant; provided, that the
failure of the holder hereof to make any such request shall not affect the
continuing obligation of the Company to the holder hereof in respect of such
rights.

15.  Lost Warrants or Stock Certificates.  The Company covenants to the holder
hereof that, upon receipt of evidence reasonably satisfactory to the Company of
the loss, theft, destruction or mutilation of this Warrant or any stock
certificate and, in the case of any such loss, theft or destruction, upon
receipt of an indemnity reasonably satisfactory to the Company, or in the case
of any such mutilation upon surrender and cancellation of such Warrant or stock

                                       9.
<PAGE>

certificate, the Company will make and deliver a new Warrant or stock
certificate, of like tenor, in lieu of the lost, stolen, destroyed or mutilated
Warrant or stock certificate.

16.  Descriptive Headings.  The descriptive headings of the several paragraphs
of this Warrant are inserted for convenience only and do not constitute a part
of this Warrant.  The language in this Warrant shall be construed as to its fair
meaning without regard to which party drafted this Warrant.

17.  Governing Law.  This Warrant shall be construed and enforced in accordance
with, and the rights of the parties shall be governed by, the laws of the State
of California; provided, however, that any matters herein dealing with the
internal corporate governance of the Company or the rights, preferences and
privileges applicable to the Company's capital stock shall be governed by the
laws of the State of Delaware.

18.  Survival of Representations.  Warranties and Agreements.  All
representations and warranties of the Company and the holder hereof contained
herein shall survive the Date of Grant, the exercise or conversion of this
Warrant (or any part hereof) or the termination or expiration of rights
hereunder.  All agreements of the Company and the holder hereof contained herein
shall survive indefinitely until, by their respective terms, they are no longer
operative.

19.  Remedies.  In case any one or more of the covenants and agreements
contained in this Warrant shall have been breached, the holders hereof (in the
case of a breach by the Company), or the Company (in the case of a breach by a
holder), may proceed to protect and enforce their or its rights either by suit
in equity and/or by action at law, including, but not limited to, an action for
damages as a result of (?)

20.  No Impairment of Rights.  The Company will not, by amendment of its Charter
or through any other means, 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 action as
may be necessary or appropriate in order to protect the rights of the holder of
this Warrant against impairment.

21.  Severability.  The invalidity or unenforceability of any provision of this
Warrant in any jurisdiction shall not affect the validity or enforceability of
such provision in any other jurisdiction, or affect any other provision of this
Warrant, which shall remain in full force and effect.

22.  Recovery of Litigation Costs. If any legal action or other proceeding is
brought for the enforcement of this Warrant, or because of an alleged dispute,
breach, default, or misrepresentation in connection with any of the provisions
of this Warrant, the successful or prevailing party or parties shall be entitled
to recover reasonable attorneys' fees and other costs incurred in that action or
proceeding in addition to any other relief to which it or they may be entitled.

23.  Entire Agreement: Modification. This Warrant constitutes the entire
agreement between the parties pertaining to the subject matter contained in it
and supersedes all prior and contemporaneous agreements, representations, and
undertakings of the parties, whether oral or written, with respect to such
subject matter.

                                      10.
<PAGE>

                              EXELIXIS PHARMACEUTICALS, INC.,
                              a Delaware corporation

                              By:  /s/ Remi Barbier
                                 ---------------------------------------
                                 Remi Barbier, Chief Operating Officer

                              Address: 260 Littlefield Avenue
                                       South San Francisco, CA 94080

                                      11.
<PAGE>

                                EXHIBIT A

                            NOTICE OF EXERCISE

To:  EXELIXIS PHARMACEUTICALS, INC. (the "Company")

     1.   The undersigned hereby:

          [_]  elects to purchase __ shares of Common Stock of the Company
               pursuant to the terms of the attached Warrant, and tenders
               herewith payment of the purchase price of such shares in
               full, or

          [_]  elects to exercise its net issuance rights pursuant to Section
10.3 of the attached Warrant with respect to __ shares of Common Stock.

2.   Please issue a certificate or certificates representing said shares in the
name of the undersigned or in such other name or names as are specified below:

                          ____________________________
                                     (Name)

                          ____________________________

                          ____________________________
                                   (Address)

3.   The undersigned represents that the aforesaid shares are being acquired for
the account of the undersigned for investment and not with a view to, or for
resale in connection with, the distribution thereof and that the undersigned has
no present intention of distributing or reselling such shares, all except as in
compliance with applicable securities laws.

                                        ____________________________
                                        (Signature)

__________________
     (Date)

                                      12.
<PAGE>

                               EXHIBIT A-1

                            NOTICE OF EXERCISE

To:  EXELIXIS PHARMACEUTICALS, INC. (the "Company")

1.   Contingent upon and effective immediately prior to the closing (the
"Closing") of the Company's public offering contemplated by the Registration
Statement on Form S_______ , filed _______________________, 19___, the
undersigned hereby:

     [_]  elects to purchase shares of Common Stock of the Company (or such
lesser number of shares as may be sold on behalf of the undersigned at the
Closing) pursuant to the terms of the attached Warrant, or

     [_]  elects to exercise its net issuance rights pursuant to Section 10.3 of
the attached Warrant with respect to ____ Shares of Common Stock.

2.   Please deliver to the custodian for the selling shareholders a stock
certificate representing such _________ shares.

3.   The undersigned has instructed the custodian for the selling shareholders
to deliver to the Company $___ or, if less, the net proceeds due the undersigned
from the sale of shares in the aforesaid public offering.  If such net proceeds
are less than the purchase price for such shares, the undersigned agrees to
deliver the difference to the Company prior to the Closing.

                                         ____________________________
                                         (Signature)

_______________
    (Date)

                                      13.

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