Document:

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                                                                     EXHIBIT 4.3

THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE BEEN ACQUIRED FOR INVESTMENT
AND HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933 OR ANY STATE
SECURITIES LAWS. THEY MAY NOT BE SOLD, OFFERED FOR SALE, PLEDGED, OR
HYPOTHECATED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT RELATED
THERETO OR AN OPINION OF COUNSEL (WHICH MAY BE COMPANY COUNSEL) REASONABLY
SATISFACTORY TO THE COMPANY THAT SUCH REGISTRATION IS NOT REQUIRED UNDER THE
SECURITIES ACT OF 1933 OR ANY STATE SECURITIES LAWS.

                              WARRANT AGREEMENT

            To Purchase Shares of the Series A Preferred Stock of

                        EXELIXIS PHARMACEUTICALS, INC.

         Originally Dated as of July 20, 1995 (the "Effective Date")
                        Re-Issued as of August 17, 1998

     Whereas, Exelixis Pharmaceuticals, Inc., a Delaware corporation (the
"Company"), has entered into a Master Lease Agreement dated as of June 12, 1995,
Equipment Schedules No. VL-1 dated as of May 3, 1995, and Equipment Schedules
No. VL-2 and VL.-3 dated as of June 12, 1995, and related Schedules
(collectively the "Leases") with Comdisco, Inc., a Delaware corporation (the
"Warrantholder"); and

     Whereas, in consideration for such Leases, the Company entered into a
Warrant Agreement dated as of July 20, 1995 (the "Original Warrant Agreement"),
whereby the Company granted the Warrantholder the right to purchase 188,214
shares of its Series A Preferred Stock; and

     Whereas, pursuant to and in accordance with the Original Warrant Agreement,
the Warrantholder has transferred to Gregory Stento, effective as of August 17,
1998, the Warrantholder's rights under the Original Warrant Agreement with
respect to the purchase of 20,486 shares of the Company's Series A Preferred
Stock (the "Warrant Transfer"); and

     Whereas, the Company and the Warrantholder acknowledge the Warrant Transfer
and, accordingly, the Company is reissuing, as of August 17, 1998, the Warrants
provided for in the Original Warrant Agreement, and the Company and the
Warrantholder are entering into this Warrant Agreement, to reflect the Warrant
Transfer and the Warrantholder's right to purchase 167,728 shares of Series A
Preferred Stock as set forth herein;

     Now, Therefore, in consideration of the foregoing, and the mutual covenants
and agreements contained herein, the Company and Warrantholder agree as follows:

1.   Grant Of The Right To Purchase Preferred Stock.

     The Company hereby grants to the Warrantholder, and the Warrantholder is
entitled, upon the terms and subject to the conditions hereinafter set forth, to
subscribe to and purchase, from the Company, 167,728 fully paid and non-
assessable shares of the Company's Preferred

                                       1.
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Stock at a purchase price of $.70 per share (the "Exercise Price"). The number
and purchase price of such shares are subject to adjustment as provided in
Section 8 hereof.

2.   Term Of The Warrant Agreement.

     Except as otherwise provided for herein, the term of this Warrant Agreement
and the right to purchase Preferred Stock as granted herein shall commence on
the Effective Date and shall be exercisable for a period of (i) ten (10) years
or (ii) five (5) years from the effective date of the Company's initial public
offering, whichever is longer.  Notwithstanding anything to the contrary
contained above, in the event that this Warrant has not been exercised on or
before the Company's initial public offering, this Warrant shall automatically
convert to a Warrant for shares of the Company's Common Stock, and the Company
and the Warrantholder agree to execute a new Warrant Agreement reflecting such
conversion.

3.   Exercise Of The Purchase Rights.

     The purchase rights set forth in this Warrant Agreement are exercisable by
the Warrantholder, in whole or in part (but not for a fraction of a share), at
any time, or from time to time, prior to the expiration of the term set forth in
Section 2 above, by tendering to the Company at its principal office a notice of
exercise in the form attached hereto as Exhibit I (the "Notice of Exercise"),
duly completed and executed.  Promptly upon receipt of the Notice of Exercise
and the payment of the purchase price in accordance with the terms set forth
below, and in no event later than thirty (30) days thereafter, the Company shall
issue to the Warrantholder a certificate for the number of shares of Preferred
Stock purchased and shall execute the Notice of Exercise indicating the number
of shares which remain subject to future purchases, if any.

     The Exercise Price for the number of shares of Preferred Stock to be
purchased by the Warrantholder may be paid at the Warrantholder's election
either (i) by cash or check, or (ii) by surrender of warrants ("Net Issuance")
as determined below.  If the Warrantholder elects the Net Issuance method, the
Company will issue Preferred Stock in accordance with the following formula:

     X = Y(A-B)
         ------
           A

Where: X =  the number of shares of Preferred Stock to be issued to the
Warrantholder.

     Y =  the number of shares of Preferred Stock requested to be exercised
          under this warrant Agreement.

     A =  the fair market value of one (1) share of Common Stock.

     B =  the Exercise Price.

     As used herein, current fair market value of common Stock as of a
particular date (the "Determination Date") shall mean with respect to each share
of Common Stock:

                                       2.
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          (i)   if the exercise is in connection with an initial public
offering, and if the company's Registration Statement relating to such public
offering has been declared effective by the Securities and Exchange Commission
("SEC"), then the initial "Price to Public" specified in the final prospectus
with respect to the offering;

          (ii)  if this Warrant is exercised after, and not in connection with
the company's initial public offering, and:

     (a)  if traded on a securities exchange, the fair market value shall be
deemed to be the average of the closing prices over a twenty-one (21) day period
ending three days before the Determination Date; or

     (b)  if actively traded over-the-counter, the fair market value shall be
deemed to be the average of the closing bid and asked prices quoted on the
NASDAQ system (or similar system) over the twenty-one (21) day period ending
three days before the Determination Date;

          (iii) if at any time the Common Stock is not listed on any securities
exchange or quoted in the NASDAQ System or the over-the-counter market, the
current fair market value of Common Stock shall be the highest price per share
which the Company could obtain from a willing buyer (not a current employee or
director) for shares of Common Stock sold by the Company, from authorized but
unissued shares, as determined in good faith by its Board of Directors, unless
the Company shall become subject to a merger, acquisition or other consolidation
pursuant to which the Company is not the surviving party, in which case the fair
market value of Common Stock shall be deemed to be the value received by the
holders of the Company's Preferred Stock on a common equivalent basis pursuant
to such merger or acquisition.

          Upon partial exercise of this Warrant by either cash or Net Issuance,
the Company shall promptly issue an amended Warrant Agreement representing the
remaining number of shares purchasable hereunder.  All other terms and
conditions of such amended Warrant Agreement shall be identical to those
contained herein, including, but not limited to the Effective Date hereof.

4.   Reservation Of Shares.

     (a) Authorization and Reservation of Shares. During the term of this
Warrant Agreement, the Company will at all times have authorized and reserved a
sufficient number of shares of its Preferred Stock to provide for the exercise
of the rights to purchase Preferred Stock as provided for herein.

     (b) Registration or Listing. If any shams of Preferred Stock required to be
reserved hereunder require registration with or approval of any governmental
authority under any Federal or State law (other than any registration under the
Securities Act of 1933, as amended (the "1933 Act") as then in effect, or any
similar Federal statute then enforced, or any state securities law, required by
reason of any transfer involved in such conversion), or listing on any domestic
securities exchange, before such shares may be issued upon conversion, the
Company will, at its expense and as expeditiously as possible, use its best
efforts to cause such shares to be duly

                                       3.
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registered, listed or approved for listing on such domestic securities exchange,
as the case maybe.

5.   No Fractional Shares Or Scrip.

     No fractional shares or scrip representing fractional shares shall be
issued upon the exercise of the Warrant, but in lieu of such fractional shares
the Company shall make a cash payment therefor upon the basis of the Exercise
Price then in effect.

6.   No Rights As Shareholder.

     This Warrant Agreement does not entitle the Warrantholder to any voting
rights or other rights as a shareholder of the Company prior to the exercise of
the Warrant. No dividends or interest shall be payable or accrued in respect of
this warrant or the interest represented hereby or the shares purchasable
hereunder until, and only to the extent that this Warrant shall have been
exercised.

7.   Warrantholder Registry.

     The Company shall maintain a registry showing the name and address of the
registered holder of this Warrant Agreement.

8.   Adjustment Rights.

     The Exercise Price and the number of shares of Preferred Stock purchasable
hereunder are subject to adjustment, as follows:

     (a) Merger and Sale of Assets.  If at any time there shall be a capital
reorganization of the shares of the Company's stock (other than a combination,
reclassification, exchange or subdivision of shares otherwise provided for
herein), or a merger or consolidation of the Company with or into another
corporation when the Company is not the surviving corporation, or the sale of
all or substantially all of the Company's properties and assets to any other
person (hereinafter referred to as a "Merger Event"), then, as a part of such
Merger Event, lawful provision shall be made so that the Warrantholder shall
thereafter be entitled to receive, upon exercise of the Warrant, the number of
shares of preferred stock or other securities of the successor corporation
resulting from such Merger Event, equivalent in value to that which would have
been issuable if Warrantholder had exercised this Warrant immediately prior to
the Merger Event.  In any such case, appropriate adjustment (as determined in
good faith by the Company's Board of Directors) shall be made in the application
of the provisions of this Warrant Agreement with respect to the rights and
interest of the Warrantholder after the Merger Event to the end that the
provisions of this Warrant Agreement (including adjustments of the Exercise
Price and number of shares of Preferred Stock purchasable) shall be applicable
to the greatest extent possible.

     (b) Reclassification of Shares.  If the Company at any time shall, by
combination, reclassification, exchange or subdivision of securities or
otherwise, change any of the securities as to which purchase rights under this
Warrant Agreement exist into the same or a different number of securities of any
other class or classes, this Warrant Agreement shall thereafter

                                       4.
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represent the right to acquire such number and kind of securities as would have
been issuable as the result of such change with respect to the securities which
were subject to the purchase rights under this Warrant Agreement immediately
prior to such combination, reclassification, exchange, subdivision or other
change.

     (c) Subdivision or Combination of Shares.  If the Company at any time shall
combine or subdivide its Preferred Stock, the Exercise Price shall be
proportionately decreased in the case of a subdivision, or proportionately
increased in the case of a combination.

     (d) Stock Dividends. If the Company at any time shall pay a dividend
payable in, or make any other distribution (except any distribution specifically
provided for in the foregoing subsections (a) or (b)) of the Company's stock,
then the Exercise Price shall be adjusted, from and after the record date of
such dividend or distribution, to that price determined by multiplying the
Exercise Price in effect immediately prior to such record date by a fraction (i)
the numerator of which shall be the total number of all shares of the Company's
stock outstanding immediately prior to such dividend or distribution, and (ii)
the denominator of which shall be the total number of all shares of the
Company's stock outstanding immediately after such dividend or distribution. The
Warrantholder shall thereafter be entitled to purchase, at the Exercise Price
resulting from such adjustment, the number of shares of Preferred Stock
(calculated to the nearest whole share) obtained by multiplying the Exercise
Price in effect immediately prior to such adjustment by the number of shares of
Preferred Stock issuable upon the exercise hereof immediately prior to such
adjustment and dividing the product thereof by the Exercise Price resulting from
such adjustment.

     (e) Antidilution Rights.  Additional antidilution rights applicable to the
Preferred Stock purchasable hereunder are as sat forth in the Company's Restated
Certificate of Incorporation, as amended through the Effective Date, a true and
complete copy of which is attached hereto as Exhibit III (the "Charter").  The
Company shall promptly provide the Warrantholder with any restatement,
amendment, modification or waiver of the Charter.  The Company shall provide
Warrantholder with prior written notice of any issuance of its stock or other
equity security to occur after the Effective Date of this Warrant, to the extent
that the Company is required to notify the holders of its Preferred Stock.

     (f) Notice of Adjustments. If: (i) the Company shall declare any dividend
or distribution upon its stock, whether in cash, property, stock or other
securities; (ii) the Company shall offer for subscription pro rata to the
holders of any class of its Preferred or other convertible stock any additional
shares of stock of any class or other rights; (iii) there shall be any Merger
Event; or (iv) there shall be any voluntary or involuntary dissolution,
liquidation or winding up of the Company; then, in connection with each such
event, the Company shall send to the Warrantholder: (A) at least fifteen (15)
days' prior written notice of the date on which the books of the Company shall
close or a record shall be taken for such dividend, distribution, subscription
rights (specifying the date on which the holders of Preferred Stock shall be
entitled thereto) or for determining rights to vote in respect of such Merger
Event, dissolution, liquidation or winding up; and (B) in the case of any such
Merger Event, dissolution, liquidation or winding up, at least fifteen (15)
days' prior written notice of the date when the same shall take place (and
specifying the date on which the holders of Preferred Stock shall be entitled to
exchange their Preferred Stock for securities or other property deliverable upon
such Merger Event, dissolution,

                                       5.
<PAGE>

liquidation or winding up). In the case of a public offering, the Company shall
give Warrantholder at least fifteen (15) days written notice prior to the
effective date thereof.

     Each such written notice shall set forth, in reasonable detail, (i) the
event requiring the adjustment, (ii) the amount of the adjustment, (iii) the
method by which such adjustment was calculated, (iv) the Exercise Price, and (v)
the number of shares subject to purchase hereunder after giving effect to such
adjustment, and shall be given by first class mail, postage prepaid, addressed
to the Warrantholder, at the address as shown on the books of the Company.

     (g) Timely Notice.  Failure to timely provide such notice required by
subsection (g) above shall entitle Warrantholder to retain the benefit of the
applicable notice period notwithstanding anything to the contrary contained in
any insufficient notice received by Warrantholder.  The notice period shall
begin on the date Warrantholder actually receives a written notice containing
all the information specified above.

     (h) No Adjustments.  No adjustment of the Exercise Price or the number of
shares of Preferred Stock purchasable under this Warrant Agreement shall be
effected with respect to: (i) shares of Common Stock issued or issuable upon
conversion of shares of Preferred Stock; (ii) shares of Common Stock issued or
issuable to officers, employees or directors of, or consultants to, the Company
pursuant to a stock purchase or option plan or other employee stock bonus
arrangement (collectively, the "Plans") approved by the Board of Directors;
(iii) shares of common Stock or Preferred Stock issuable pursuant to warrants
outstanding as of the date hereof (notwithstanding any subsequent transfer of
all or part of such warrants); (iv) shares of Common Stock or Preferred Stock
issued or issuable pursuant to warrants issued in connection with the
establishment of credit facilities for the Company (including, without
limitation, in connection with equipment leasing arrangements); or (v) shares of
Common Stock or Preferred Stock issued in connection with corporate partnering
relationships or joint ventures approved by the Company's Board of Directors.

9.   Representations, Warranties And Covenants Of The Company.

     (a) Reservation of Preferred Stock.  The Preferred Stock issuable upon
exercise of the Warrantholder's rights has been duly and validly reserved and,
when issued and paid for by the Warrantholder in accordance with the provisions
of this Warrant Agreement, will be validly issued, fully paid and non-
assessable, and will be free of any taxes, liens, charges or encumbrances of any
nature whatsoever, provided, however, that the Preferred Stock issuable pursuant
to this Warrant Agreement may be subject to restrictions on transfer under state
and/or Federal securities laws.  The Company has made available to the
Warrantholder true, correct and complete copies of its Charter and Bylaws, as
amended, and minutes of all Board of Directors (including all committees of the
Board of Directors, if any) and Shareholder meetings from January, 1995 through
July, 1995.  The issuance of certificates for shares of Preferred Stock upon
exercise of the Warrant Agreement shall be made without charge to the
Warrantholder for any issuance tax in respect thereof, or other cost incurred by
the Company in connection with such exercise and the related issuance of shares
of Preferred Stock.  The Company shall not be required to pay any tax which may
be payable in respect of any transfer involved and the issuance and delivery of
any certificate in a name other than that of the Warrantholder.

                                       6.
<PAGE>

     (b) Due Authority. The execution and delivery by the Company of this
Warrant Agreement and the performance of all obligations of the Company
hereunder, including the issuance to Warrantholder of the right to acquire the
shares of Preferred Stock, have been duly authorized by all necessary corporate
action on the part of the Company, and the Leases and this Warrant Agreement are
not inconsistent with the Company's Charter or Bylaws, do not contravene any
material law or governmental rule, regulation or order applicable to it, do not
and will not contravene any provision of, or constitute a default under, any
material indenture, mortgage, contract or other instrument to which it is a
party or by which it is bound, and the Leases and this Warrant Agreement
constitute legal, valid and binding agreements of the Company, enforceable in
accordance with their respective terms, subject to laws of general application
from time to time in effect affecting creditor's rights and the exercise of
judicial discretion in accordance with general equitable principles.

     (c) Consents and Approvals. No consent or approval of, giving of notice to,
registration with, or taking of any other action in respect of any state,
Federal or other governmental authority or agency is required with respect to
the execution, delivery and performance by the Company of its obligations under
this Warrant Agreement, except for the filing of notices as required by
applicable federal and state securities laws, which filings will be effective by
the time required thereby.

     (d) Issued Securities.  All issued and outstanding shares of Common Stock,
Preferred Stock or any other securities of the Company have been duly authorized
and validly issued and are fully paid and nonassessable.  All outstanding shares
of Common Stock, Preferred Stock and any other securities were issued in full
compliance with, or were exempt from, all Federal and state securities laws,
assuming the accuracy of all representations made by the purchasers thereof.  In
addition, as of the Effective Date:

         (i)   The authorized capital of the Company consists of (A) 20,000,000
shares of Common Stock, of which 950,000 shares we issued and outstanding, (B)
526,819 shares of Class B Common Stock, all of which are issued and outstanding,
and (C) 7,000,000 shares of Preferred Stock, of which 5,328,571 shares are
issued and outstanding and are convertible into 5,328,517 shares of Common Stock
at $0.70 per share.

         (ii)  The Company has reserved 1,350,000 shares of Common Stock for
issuance under its 1994 Employee, Director and Consultant Stock Plan, under
which 665,000 options or rights to purchase Common Stock are currently
outstanding. Except for 92,858 warrants to purchase Common Stock outstanding as
of the date hereof and Common Stock conversion rights and certain rights of
first refusal in favor of the current holders of the Preferred Stock, there are
no other options, warrants, conversion privileges or other rights presently
outstanding to purchase or otherwise acquire any authorized but unissued shares
of the Company's capital stock or other securities of the Company.

         (iii) Except for certain rights of first refusal in favor of currant
holders of the Preferred Stock, no shareholder of the Company has preemptive
rights to purchase new issuances of the Company's capital stock.

                                       7.
<PAGE>

     (e) Insurance. The Company has in full force and effect insurance policies,
with extended coverage, insuring the Company and its property and business
against such material losses and risks, and in such amounts, as are customary
for corporations engaged in a similar business and similarly situated and as
otherwise may be required pursuant to the terms of any other contract or
agreement.

     (f) Other Commitments to Register Securities.  As of the Effective Date,
except as set forth in this Warrant Agreement and its Registration Rights
Agreement with current holders of its Preferred Stock, the Company is not,
pursuant to the terms of any other agreement currently in existence, under any
obligation to register under the 1933 Act any of its presently outstanding
securities or any of its securities which may hereafter be issued.

     (g) Exempt Transaction.  Subject to the accuracy of the Warrantholder's
representations in Section 10 hereof, the issuance of the Preferred Stock upon
exercise of this Warrant will constitute a transaction exempt from (i) the
registration requirements of Section 5 of the 1933 Act, in reliance upon Section
4(2) thereof, and (ii) applicable state securities laws.

     (h) Compliance with Rule 144.  At the written request of the Warrantholder,
who proposes to sell Preferred Stock issuable upon the exercise of the Warrant
in compliance with Rule 144 promulgated by the Securities and Exchange
Commission, the Company shall furnish to the Warrantholder, within ten days
after receipt of such request, a written statement indicating if the Company is
in compliance with the filing requirements of the Securities and Exchange
Commission as set forth in such Rule, as such Rule may be amended from time to
time.

10.  Representations And Covenants Of The Warrantholder.

     This Warrant Agreement has been entered into by the Company in reliance
upon the following representations and covenants of the Warrantholder:

     (a) Investment Purpose. The right to acquire Preferred Stock or the
Preferred Stock issuable upon exercise of the Warrantholder's rights contained
herein will be acquired for investment and not with a view to the sale or
distribution of any part thereof, and the Warrantholder has no present intention
of selling or engaging in any public distribution of the same except pursuant to
a registration or exemption.

     (b) Private Issue. The Warrantholder understands (i) that the Preferred
Stock issuable upon exercise of this Warrant is not registered under the 1933
Act or qualified under applicable state securities laws on the ground that the
issuance contemplated by this Warrant Agreement will be exempt from the
registration and qualifications requirements thereof, and (ii) that the
Company's reliance on such exemption is predicated on the representations set
forth in this Section 10.

     (c) Disposition of Warrantholder's Rights. In no event will the
Warrantholder make a disposition of any of its rights to acquire Preferred Stock
or Preferred Stock issuable upon exercise of such rights unless and until (i) it
shall have notified the Company of the proposed disposition, and (ii) if
requested by the Company, it shall have furnished the Company with an opinion of
counsel (which counsel may either be inside or outside counsel to the
Warrantholder) satisfactory to the Company and its counsel to the effect that
(A) appropriate

                                       8.
<PAGE>

action necessary for compliance with the 1933 Act has been taken, or (B) an
exemption from the registration requirements of the 1933 Act is available.
Notwithstanding the foregoing, the restrictions imposed upon the transferability
of any of its rights to acquire Preferred Stock or Preferred Stock issuable on
the exercise of such rights do not apply to transfers from the beneficial owner
of any of the aforementioned securities to its nominee or from such nominee to
its beneficial owner, and shall terminate as to any particular share of
Preferred Stock when (1) such security shall have been effectively registered
under the 1933 Act and sold by the holder thereof in accordance with such
registration or (2) such security shall have been sold without registration in
compliance with Rule 144 under the 1933 Act, or (3) a letter shall have been
issued to the Warrantholder at its request by the staff of the SEC or a ruling
shall have been issued to the Warrantholder at its request by the SEC stating
that no action shall be recommended by such staff or taken by the SEC, as the
case may be, if such security is transferred without registration under the 1933
Act in accordance with the conditions set forth in such letter or ruling and
such letter or ruling specifies that no subsequent restrictions on transfer we
required. Whenever the restrictions imposed hereunder shall terminate, as
hereinabove provided, the Warrantholder or holder of a share of Preferred Stock
then outstanding as to which such restrictions have terminated shall be entitled
to receive from the Company, without expense to such holder, one or more new
certificates for the Warrant or for such shares of Preferred Stock not bearing
any restrictive legend.

     (d) Financial Risk.  The Warrantholder has such knowledge and experience in
financial and business matters as to be capable of evaluating the merits and
risks of its investment, and has the ability to bear the economic risks of its
investment.

     (e) Risk of No Registration.  The Warrantholder understands that if the
Company does not register with the SEC pursuant to Section 12 of the 1933 Act,
or file reports pursuant to Section 15(d), of the Securities Exchange Act of
1934 (the "1934 Act"), or if a registration statement covering the securities
under the 1933 Act is not in effect when it desires to sell (i) the rights to
purchase Preferred Stock pursuant to this Warrant Agreement, or (ii) the
Preferred Stock issuable upon exercise of the right to purchase, it may be
required to hold such securities for an indefinite period.  The Warrantholder
also understands that any sale of its rights of the Warrantholder to purchase
Preferred Stock or Preferred Stock which might be made by it in reliance upon
Rule 144 under the 1933 Act may be made only in accordance with the terms and
conditions of that Rule.

11.  Transfers.

     Subject to the terms and conditions contained in Section 10 hereof, this
Warrant Agreement and all rights hereunder are transferable in whole or in part
by the Warrantholder and any successor transferee, provided, however, in no
event shall the number of transfers of the rights and interests in all of the
Warrants exceed three (3) transfers.  The transfer shall be recorded on the
books of the Company upon receipt by the Company of a notice of transfer in the
form attached hereto as Exhibit II (the "Transfer Notice"), at its principal
offices and the payment to the Company of all transfer taxes and other
governmental charges imposed on such transfer.  When this Warrant shall have
been so transferred pursuant to Section 11, the holder hereof may be treated by
the Company and all other persons dealing with this Warrant as the absolute
owner and holder hereof for any purpose and as the person entitled to exercise
the rights represented by

                                       9.
<PAGE>

this Warrant, or to the registration of transfer hereof on the books of the
Company;, and until due presentment for registered holders hereof as the owner
and holder for all purposes, and the Company shall not be affected by notice to
the contrary.

12.  Miscellaneous.

     (a) Effective Date.  The provisions of this Warrant Agreement shall be
construed and shall be given effect in all respects as if it had been executed
and delivered by the Company on the date hereof.  This Warrant Agreement shall
be binding upon any successors or assigns of the Company.

     (b) Attorney's Fees.  In any litigation, arbitration or court proceeding
between the Company and the Warrantholder relating hereto, the prevailing party
shall be entitled to attorneys' fees and expenses and all costs of proceedings
incurred in enforcing this Warrant Agreement.

     (c) Governing Law. This Warrant Agreement shall be governed by and
construed for all purposes under and in accordance with the laws of the State of
Illinois.

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

     (e) Notices.  Any notice required or permitted hereunder shall be given in
writing and shall be deemed effectively given upon personal delivery, facsimile
transmission (provided that the original is sent by personal delivery or mail as
hereinafter set forth) or seven (7) days after deposit in the United States
mail, by registered or certified mail, addressed (i) to the Warrantholder at
6111 North River Road, Rosemont, Illinois 60018, attention: James Labe, Venture
Leasing Director, cc:  Legal Department (and/or, if by facsimile, (847) 518-
5465) and (ii) to the Company at One Kendall Square, Building 600, Cambridge,
Massachusetts 02139, attention: President (and/or if by facsimile, (650) 825-
2205) or at such other address as any such party may subsequently designate by
written notice to the other party.

     (f) Remedies. In the event of any default hereunder, the non-defaulting
party may proceed to protect and enforce 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 default, and/or an action for specific performance for any
default where such non-defaulting party will not have an adequate remedy at law
and where damages will not be readily ascertainable. The Company expressly
agrees that it shall not oppose an application by the Warrantholder or any other
person entitled to the benefit of this Agreement requiring specific performance
of any or all provisions hereof or enjoining the Company from continuing to
commit any such breach of this Agreement.

     (g) 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
actions as may be necessary or appropriate in order to protect the rights of the
Warrantholder against impairment.

                                      10.
<PAGE>

     (h) Survival.  The representations, warranties, covenants and conditions of
the respective parties contained herein or made pursuant to this Warrant
Agreement shall survive the execution and delivery of this Warrant Agreement.

     (i) Severability.  In the event any one or more of the provisions of this
Warrant Agreement shall for any reason be held invalid, illegal or
unenforceable, the remaining provisions of this Warrant Agreement shall be
unimpaired, and the invalid, illegal or unenforceable provision shall be
replaced by a mutually acceptable valid, legal and enforceable provision, which
comes closest to the intention of the parties underlying the invalid, illegal or
unenforceable provision.

     (j) Amendments; Headings.  Any provision of this Warrant Agreement may be
amended by a written instrument signed by the Company and by the Warrantholder.
The headings in this Warrant Agreement are for purposes of reference only, and
shall not limit or otherwise affect any of the terms hereof.

     (k) Additional Documents. The Company, upon execution of this Warrant
Agreement, shall provide the Warrantholder with certified resolutions with
respect to the representations, warranties and covenants set forth in
subparagraphs (a) through (d), (f) and (g) of Section 9 above. The Company shall
also supply such other documents as the Warrantholder may from time to time
reasonably request

           [THE REMAINDER OF THIS PAGE WAS INTENTIONALLY LEFT BLANK]

                                      11.
<PAGE>

     In Witness Whereof, the parties hereto have caused this Warrant Agreement
to be executed by its officers thereunto duly authorized as of the Effective
Date.

                      Company:    EXELIXIS PHARMACEUTICALS, INC.

                                  By: /s/ George A. Scangos
                                     --------------------------------------

                                  Title: President, CEO
                                        -----------------------------------

                      Warrantholder,  COMDISCO, INC.

                                  By: /s/ Joel J. Vosicky
                                     --------------------------------------

                                  Title: Senior Vice President and Chief
                                         Financial Officer
                                        -----------------------------------

                                      12.
<PAGE>

                                   EXHIBIT I

                              NOTICE OF EXERCISE

To:__________________

(1)  The undersigned Warrantholder hereby elects to purchase ____ shares of the
     Series A Preferred Stock of Exelixis Pharmaceuticals, Inc., pursuant to the
     terms of the Warrant Agreement dated the 17th day of August, 1998 (the
     "Warrant Agreement") between Exelixis Pharmaceuticals, Inc. and the
     Warrantholder, and tenders herewith payment of the purchase price for such
     shares in full, together with all applicable transfer taxes, if any.

(2)  In exercising its rights to purchase the Preferred Stock of Exelixis
     Pharmaceuticals, Inc., the undersigned hereby confirms and acknowledges the
     investment representations and warranties made in Section 10 of the Warrant
     Agreement.

(3)  Please issue a certificate or certificates representing said shares of
     Series A Preferred Stock in the name of the undersigned or in such other
     name as is specified below.

____________________________________

(Name)

____________________________________

(Address)

Warrantholder: COMDISCO, INC.

By:_________________________________

Title:______________________________

Date:_______________________________

                                      13.
<PAGE>

                          ACKNOWLEDGMENT OF EXERCISE

     The undersigned ______, hereby acknowledges receipt of the "Notice of
Exercise" from Comdisco, Inc., to purchase  shares of the Series A Preferred
Stock of Exelixis Pharmaceuticals, Inc., pursuant to the terms of the Warrant
Agreement and further acknowledges that _____ shares remain subject to purchase
under the terms of the Warrant Agreement

                           Company: Exelexis Pharmaceuticals, Inc.

                           By:____________________________________

                           Title:_________________________________

                           Date:__________________________________

                                      14.
<PAGE>

                                  EXHIBIT II

                                TRANSFER NOTICE

     (To transfer or assign the foregoing Warrant Agreement execute this form
and supply required information.  Do not use this form to purchase shares.)

     FOR VALUE RECEIVED, the foregoing Warrant Agreement and all rights
evidenced thereby are hereby transferred and assigned to

________________________________________________________________________________
(Please Print)

whose address is________________________________________________________________

________________________________________________________________________________

                Dated___________________________________________________________

                Holder's Signature______________________________________________

                Holder's Address________________________________________________

Signature Guaranteed:___________________________________________________________

NOTE:     The signature to this Transfer Notice must correspond with the name as
          it appears on the face of the Warrant Agreement.  Without alteration
          or enlargement or any change whatever.  Officers of corporations and
          those acting in a fiduciary or other representative capacity should
          file proper evidence of authority to assign the foregoing Warrant
          Agreement.

                                      15.<PAGE>

                                                                     EXHIBIT 4.4

THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE BEEN ACQUIRED FOR INVESTMENT
AND HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933 OR ANY STATE
SECURITIES LAWS. THEY MAY NOT BE SOLD, OFFERED FOR SALE, PLEDGED, OR
HYPOTHECATED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT RELATED
THERETO OR AN OPINION OF COUNSEL (WHICH MAY BE COMPANY COUNSEL) REASONABLY
SATISFACTORY TO THE COMPANY THAT SUCH REGISTRATION IS NOT REQUIRED UNDER THE
SECURITIES ACT OF 1933 OR ANY STATE SECURITIES LAWS.

                               WARRANT AGREEMENT

             To Purchase Shares of the Series A Preferred Stock of

                        EXELIXIS PHARMACEUTICALS, INC.

          Originally Dated as of July 20, 1995 (the 'Effective Date")
                        Re-Issued as of August 17, 1998

     Whereas, Exelixis Pharmaceuticals, Inc., a Delaware corporation (the
"Company"), has entered into this Warrant Agreement dated as of July 20, 1995
(the "Original Warrant Agreement") with Comdisco, Inc. (the "Original
Warrantholder"), whereby the Company granted the Original Warrantholder the
right to purchase shares of the Company's Series A Preferred Stock;

     Whereas, pursuant to and in accordance with the Original Warrant Agreement,
the Original Warrantholder has transferred to Gregory Stento (the
"Warrantholder"), effective as of August 17, 1998, the Original Warrantholder's
rights under the Original Warrant Agreement with respect to the purchase of
20,486 shares of the Company's Series A Preferred Stock (the Warrant
Transfer'); and

     Whereas, the Company and the Warrantholder acknowledge the Warrant Transfer
and, accordingly, are entering into this Warrant Agreement to reflect the
Warrant Transfer and the Warrantholder's right to purchase 20,486 shares of
Series A Preferred Stock as set forth herein;

     Now, Therefore, in consideration of mutual covenants and agreements
contained herein, the Company and Warrantholder agree as follows:

1.   Grant Of The Right To Purchase Preferred Stock.

     The Company hereby grants to the Warrantholder, and the Warrantholder is
entitled, upon the terms and subject to the conditions hereinafter set forth, to
subscribe to and purchase, from the Company, 20,486 fully paid and non-
assessable shares of the Company's Preferred Stock at a purchase price of $.70
per share (the "Exercise Price"). The number and purchase price of such shares
are subject to adjustment as provided in Section 8 hereof.

                                       1.
<PAGE>

2.   Term of The Warrant Agreement.

     Except as otherwise provided for herein, the term of this Warrant Agreement
and the right to purchase Preferred Stock as granted herein shaft commence on
the Effective Date and shaft be exercisable for a period of (i) ten (10) years
or (ii) five (5) years from the effective date of the Company's initial public
offering, whichever is longer.  Notwithstanding anything to the contrary
contained above, in the event that this Warrant has not been exercised on or
before the Company's initial public offering, this Warrant shall automatically
convert to a Warrant for shares of the Company's Common Stock, and the Company
and the Warrantholder agree to execute a new Warrant Agreement reflecting such
conversion.

3.   Exercise of The Purchase Rights.

     The purchase rights set forth in this Warrant Agreement are exercisable by
the Warrantholder, in whole or in part (but not for a fraction of a share), at
any time, or from time to time, prior to the expiration of the term set forth in
Section 2 above, by tendering to the Company at its principal office a notice of
exercise in the form attached hereto as Exhibit I (the "Notice of Exercise"),
duly completed and executed.  Promptly upon receipt of the Notice of Exercise
and the payment of the purchase price in accordance with the terms set forth
below, and in no event later than thirty (30) days thereafter, the Company shall
issue to the Warrantholder a certificate for the number of shams of Preferred
Stock purchased and shall execute the Notice of Exercise indicating the number
of shares which remain subject to future purchases, if any.

     The Exercise Price for the number of shares of Preferred Stock to be
purchased by the Warrantholder may be paid at the Warrantholder's election
either (i) by cash or check, or (ii) by surrender of Warrants ("Net Issuance")
as determined below.  If the Warrantholder elects the Net Issuance method, the
Company will issue Preferred Stock in accordance with the following formula:

     X = Y(A-B)
         _____
           A

     Where:    X =  the number of shares of Preferred Stock to be issued to the
                    Warrantholder.

               Y =  the number of shares of Preferred Stock requested to be
                    exercised under this Warrant Agreement.

               A =  the fair market value of one (1) share of Common Stock.

               B =  the Exercise Price.

     As used herein, current fair market value of Common Stock as of a
particular date (the "Determination Date") shall mean with respect to each share
of Common Stock:

               (i) if the exercise is in connection with an initial public
offering, and if the Company's Registration Statement relating to such public
offering has been declared effective by the Securities and Exchange Commission
("SEC"), then the initial "Price to Public" specified in the final prospectus
with respect to the offering;

                                       2.
<PAGE>

          (ii) if this Warrant is exercised after, and not in connection with
the Company's initial public offering, and:

     (a)  if traded on a securities exchange, the fair market value shall be
deemed to be the average of the closing prices over a twenty-one (21) day period
ending three days before the Determination Date; or

     (b)  if actively traded over-the-counter, the fair market value shall be
deemed to be the average of the closing bid and asked prices quoted on the
NASDAQ system (or similar system) over the twenty-one (21) day period ending
three days before the Determination Date;

          (iii) if at any time the Common Stock is not listed on any securities
exchange or quoted in the NASDAQ System or the over-the-counter market, the
current fair market value of Common Stock shall be the highest price per share
which the Company could obtain from a willing buyer (not a current employee or
director) for shares of Common Stock sold by the Company, from authorized but
unissued shares, as determined in good faith by its Board of Directors, unless
the Company shall become subject to a merger, acquisition or other consolidation
pursuant to which the Company is not the surviving party, in which case the fair
market value of Common Stock shall be deemed to be the value received by the
holders of the Company's Preferred Stock on a common equivalent basis pursuant
to such merger or acquisition.

     Upon partial exercise of this Warrant by either cash or Net Issuance, the
Company shall promptly issue an amended Warrant Agreement representing the
remaining number of shares purchasable hereunder.  All other terms and
conditions of such amended Warrant Agreement shall be identical to those
contained herein, including, but not limited to the Effective Date hereof.

4.   Reservation of Shares.

     (a) Authorization and Reservation Shares.  During the term of this Warrant
Agreement, the Company will at all times have authorized and reserved a
sufficient number of shares of its Preferred Stock to provide for the exercise
of the rights to purchase Preferred Stock as provided for herein.

     (b) Registration or Listing. If any shares of Preferred Stock required to
be reserved hereunder require registration with or approval of any governmental
authority under any Federal or State law (other than any registration under the
Securities Act of 1933, as amended (the "1933 Act") as then in effect, or any
similar Federal statute then enforced, or any state securities law, required by
reason of any transfer involved in such conversion), or listing on any domestic
securities exchange, before such shares may be issued upon conversion, the
Company will, at its expense and as expeditiously as possible, use its best
efforts to cause such shares to be duly registered, listed or approved for
listing on such domestic securities exchange, as the case may be.

                                       3.
<PAGE>

5.   No Fractional Shares Or Scrip.

     No fractional shares or scrip representing fractional shares shall be
issued upon the exercise of the Warrant, but in lieu of such fractional shares
the Company shall make a cash payment therefor upon the basis of the Exercise
Price then in effect.

6.   No Rights As Shareholder.

     This Warrant Agreement does not entitle the Warrantholder to any voting
rights or other rights as a shareholder of the Company prior to the exercise of
the Warrant.  No dividends or interest shall be payable or accrued in respect of
this Warrant or the interest represented hereby or the shares purchasable
hereunder until, and only to the extent that this Warrant shall have been
exercised.

7.   Warrantholder Registry.

     The Company shall maintain a registry showing the name and address of the
registered holder of this Warrant Agreement.

8.   Adjustment Rights.

     The Exercise Price and the number of shares of Preferred Stock purchasable
hereunder are subject to adjustment, as follows:

     (a) Merger and Sale of Assets.  If at any time there shall be a capital
reorganization of the shares of the Company's stock (other than a combination,
reclassification, exchange or subdivision of shares otherwise provided for
herein), or a merger or consolidation of the Company with or into another
corporation when the Company is not the surviving corporation, or the sale of
all or substantially all of the Company's properties and assets to any other
person (hereinafter referred to as a "Merger Event"), then, as a part of such
Merger Event, lawful provision shall be made so that the Warrantholder shall
thereafter be entitled to receive, upon exercise of the Warrant, the number of
shares of preferred stock or other securities of the successor corporation
resulting from such Merger Event, equivalent in value to that which would have
been issuable if Warrantholder had exercised this Warrant immediately prior to
the Merger Event.  In any such case, appropriate adjustment (as determined in
good faith by the Company's Board of Directors) shall be made in the application
of the provisions of this Warrant Agreement with respect to the rights and
interest of the Warrantholder after the Merger Event to the end that the
provisions of this Warrant Agreement (including adjustments of the Exercise
Price and number of shares of Preferred Stock purchasable) shall be applicable
to the greatest extent possible.

     (b) Reclassification of Shares.  If the Company at any time shall, by
combination, reclassification, exchange or subdivision of securities or
otherwise, change any of the securities as to which purchase rights under this
Warrant Agreement exist into the same or a different number of securities of any
other class or classes, this Warrant Agreement shall thereafter represent the
right to acquire such number and kind of securities as would have been issuable
as the result of such change with respect to the securities which were subject
to the purchase rights

                                       4.
<PAGE>

under this Warrant Agreement immediately prior to such combination,
reclassification, exchange, subdivision or other change.

     (c) Subdivision or Combination of Shares.  If the Company at any time shall
combine or subdivide its Preferred Stock, the Exercise Price shall be
proportionately decreased in the case of a subdivision, or proportionately
increased in the case of a combination.

     (d) Stock Dividends. If the Company at any time shall pay a dividend
payable in, or make any other distribution (except any distribution specifically
provided for in the foregoing subsections (a) or (b)) of the Company's stock,
then the Exercise Price shall be adjusted, from and after the record date of
such dividend or distribution, to that price determined by multiplying the
Exercise Price in effect immediately prior to such record date by a fraction (i)
the numerator of which shall be the total number of all shares of the Company's
stock outstanding immediately prior to such dividend or distribution, and (ii)
the denominator of which shall be the total number of all shares of the
Company's stock outstanding immediately after such dividend or distribution. The
Warrantholder shall thereafter be entitled to purchase, at the Exercise Price
resulting from such adjustment, the number of shares of Preferred Stock
(calculated to the nearest whole share) obtained by multiplying the Exercise
Price in effect immediately prior to such adjustment by the number of shares of
Preferred Stock issuable upon the exercise hereof immediately prior to such
adjustment and dividing the product thereof by the Exercise Price resulting from
such adjustment.

     (e) Antidilution Rights. Additional antidilution rights applicable to the
Preferred Stock purchasable hereunder are as set forth in the Company's Restated
Certificate of Incorporation as amended through the Effective Date, a true and
complete copy of which is attached hereto as Exhibit III (the "Charter").  The
Company shall promptly provide the Warrantholder with any restatement,
amendment, modification or waiver of the Charter.  The Company shall provide
Warrantholder with prior written notice of any issuance of its stock or other
equity security to occur after the Effective Date of this Warrant, to the extent
that the Company is required to notify the holders of its Preferred Stock.

     (f) Notice of Adjustments. If: (i) the Company shall declare any dividend
or distribution upon its stock, whether in cash, property, stock or other
securities; (ii) the Company shall offer for subscription prorata to the holders
of any class of its Preferred or other convertible stock any additional shares
of stock of any class or other rights; (iii) there shall be any Merger Event; or
(iv) there shall be any voluntary or involuntary dissolution, liquidation or
winding up of the Company; then, in connection with each such event, the Company
shall send to the Warrantholder: (A) at least fifteen (15) days' prior written
notice of the date on which the books of the Company shall close or a record
shall be taken for such dividend, distribution, subscription rights (specifying
the date on which the holders of Preferred Stock shall be entitled thereto) or
for determining rights to vote in respect of such Merger Event, dissolution,
liquidation or winding up; and (B) in the case of any such Merger Event,
dissolution, liquidation or winding up, at least fifteen (15) days' prior
written notice of the date when the same shall take place (and specifying the
date on which the holders of Preferred Stock shall be entitled to exchange their
Preferred Stock for securities or other property deliverable upon such Merger
Event, dissolution, liquidation or winding up). In the case of a public
offering, the Company shall give Warrantholder at least fifteen (15) days
written notice prior to the effective date thereof.

                                       5.
<PAGE>

     Each such written notice shall set forth, in reasonable detail, (i) the
event requiring the adjustment, (ii) the amount of the adjustment, (iii) the
method by which such adjustment was calculated, (iv) the Exercise Price, and (v)
the number of shares subject to purchase hereunder after giving effect to such
adjustment, and shall be given by first class mail, postage prepaid, addressed
to the Warrantholder, at the address as shown on the books of the Company.

     (g) Timely Notice.  Failure to timely provide such notice required by
subsection (g) above shall entitle Warrantholder to retain the benefit of the
applicable notice period notwithstanding anything to the contrary contained in
any insufficient notice received by Warrantholder.  The notice period shall
begin on the date Warrantholder actually receives a written notice containing
all the information specified above.

     (h) No Adjustments.  No adjustment of the Exercise Price or the number of
shares of Preferred Stock purchasable under this Warrant Agreement shall be
effected with respect to: (I) shares of Common Stock issued or issuable upon
conversion of shares of Preferred Stock; (ii) shares of Common Stock issued or
issuable to officers, employees or directors of, or consultants to, the Company
pursuant to a stock purchase or option plan or other employee stock bonus
arrangement (collectively, the "Plans") approved by the Board of Directors;
(ii) shares of Common Stock or Preferred Stock issuable pursuant to warrants
outstanding as of the date hereof (notwithstanding any subsequent transfer of
all or part of such warrants); (iv) shares of Common Stock or Preferred Stock
issued or issuable pursuant to warrants issued in connection with the
establishment of credit facilities for the Company (including, without
limitation, in connection with equipment leasing arrangements); or (v) shares of
Common Stock or Preferred Stock issued in connection with corporate partnering
relationships or joint ventures approved by the Company's Board of Directors.

9.   Representations, Warranties and Covenants of the Company.

     (a) Reservation of Preferred Stock.  The Preferred Stock issuable upon
exercise of the Warrantholder's rights has been duly and validly reserved and
when issued and paid for by the Warrantholder in accordance with the provisions
of this Warrant Agreement, will be validly issued, fully paid and non-
assessable, and will be free of any taxes, liens, charges or encumbrances of any
nature whatsoever; provided, however, that the Preferred Stock issuable pursuant
to this Warrant Agreement may be subject to restrictions on transfer under state
and/or Federal securities laws.  The Company has made available to the
Warrantholder true, correct and complete copies of its Charter and Bylaws, as
amended, and minutes of all Board of Directors (including all committees of the
Board of Directors, if any) and Shareholder meetings from January, 1995 through
July, 1995.  The issuance of certificates for shares of Preferred Stock upon
exercise of the Warrant Agreement shall be made without charge to the
Warrantholder for any issuance tax in respect thereof, or other cost incurred by
the Company in connection with such exercise and the related issuance of shares
of Preferred Stock.  The Company shall not be required to pay any tax which may
be payable in respect of any transfer involved and the issuance and delivery of
any certificate in a name other than that of the Warrantholder.

     (b) Due Authority. The execution and delivery by the Company of this
Warrant Agreement and the performance of all obligations of the Company
hereunder, including the issuance to Warrantholder of the right to acquire the
shares of Preferred Stock, have been duly

                                       6.
<PAGE>

authorized by all necessary corporate action on the part of the Company, and
this Warrant Agreement is not inconsistent with the Company's Charter or Bylaws,
does not contravene any material law or governmental rule, regulation or order
applicable to it, does not and will not contravene any provision of, or
constitute a default under, any material indenture, mortgage, contract or other
instrument to which it is a party or by which it is bound, and this Warrant
Agreement constitutes a legal, valid and binding agreement of the Company,
enforceable in accordance with its terms, subject to laws of general application
from time to time in effect affecting creditor's rights and the exercise of
judicial discretion in accordance with general equitable principles.

     (c) Consents and Approvals. No consent or approval of, giving of notice to,
registration with, or taking of any other action in respect of any state,
Federal or other governmental authority or agency is required with respect to
the execution, delivery and performance by the Company of its obligations under
this Warrant Agreement, except for the filing of notices as required by
applicable federal and state securities laws, which filings will be effective by
the time required thereby.

     (d) Issued Securities.  All issued and outstanding shares of Common Stock,
Preferred Stock or any other securities of the Company have been duly authorized
and validly issued and are fully paid and nonassessable.  All outstanding shares
of Common Stock, Preferred Stock and any other securities were issued in full
compliance with, or were exempt from, all Federal and state securities laws,
assuming the accuracy of all representations made by the purchasers thereof.  In
addition, as of the Effective Date:

         (i)   The authorized capital of the Company consists of (A) 20,000,000
shares of Common Stock, of which 950,000 shares are issued and outstanding, (B)
526,819 shares of Class B Common Stock, all of which are issued and outstanding,
and (C) 7,000,000 shares of Preferred Stock, of which 5,328,571 shares are
issued and outstanding and are convertible into 5,328,517 shares of Common Stock
at $0.70 per share.

         (ii)  The Company has reserved 1,350,000 shares of Common Stock for
issuance under its 1994 Employee, Director and Consultant Stock Plan, under
which 665,000 options or rights to purchase Common Stock are currently
outstanding. Except for 92,858 warrants to purchase Common Stock outstanding as
of the date hereof and Common Stock conversion rights and certain rights of
first refusal in favor of the current holders of the Preferred Stock, there are
no other options, warrants, conversion privileges or other rights presently
outstanding to purchase or otherwise acquire any authorized but unissued shares
of the Company's capital stock or other securities of the Company.

         (iii) Except for certain rights of first refusal in favor of current
holders of the Preferred Stock, no shareholder of the Company has preemptive
rights to purchase new issuances of the Company's capital stock.

     (e) Insurance. The Company has in full force and effect insurance policies,
with extended coverage, insuring the Company and its property and business
against such material losses and risks, and in such amounts, as are customary
for corporations engaged in a similar

                                       7.
<PAGE>

business and similarly situated and as otherwise may be required pursuant to the
terms of any other contract or agreement.

     (f) Other Commitments to Register Securities.  As of the Effective date,
except as set forth in this Warrant Agreement and its Registration Rights
Agreement with current holders of its Preferred Stock, the Company is not,
pursuant to the terms of any other agreement currently in existence, under any
obligation to register under the 1933 Act any of its presently outstanding
securities or any of its securities which may hereafter be issued.

     (g) Exempt Transaction.  Subject to the accuracy of the Warrantholder's
representations in Section 10 hereof, the issuance of the Preferred Stock upon
exercise of this Warrant will constitute a transaction exempt from (i) the
registration requirements of Section 5 of the 1933 Act, in reliance upon Section
4(2) thereof, and (ii) applicable state securities laws.

     (h) Compliance with Rule 144.  At the written request of the Warrantholder,
who proposes to sell Preferred Stock issuable upon the exercise of the Warrant
in compliance with Rule 144 promulgated by the Securities and Exchange
Commission, the Company shall furnish to the Warrantholder, within ten days
after receipt of such request, a written statement indicating if the Company is
in compliance with the filing requirements of the Securities and Exchange
Commission as set forth in such Rule, as such Rule may be amended from time to
time.

10.  Representations And Covenants Of The Warrantholder.

     This Warrant Agreement has been entered into by the Company in reliance
upon the following representations and covenants of the Warrantholder:

     (a) Investment Purpose. The right to acquire Preferred Stock or the
Preferred Stock issuable upon exercise of the Warrantholder's rights contained
herein will be acquired for investment and not with a view to the sale or
distribution of any part thereof, and the Warrantholder has no present intention
of selling or engaging in any public distribution of the same except pursuant to
a registration or exemption.

     (b) Private Issue. The Warrantholder understands (i) that the Preferred
Stock issuable upon exercise of this Warrant is not registered under the 1933
Act or qualified under applicable state securities laws on the ground that the
issuance contemplated by this Warrant Agreement will be exempt from the
registration and qualifications requirements thereof, and (ii) that the
Company's reliance on such exemption is predicated on the representations set
forth in this Section 10.

     (c) Disposition of Warrantholder's Rights. In no event will the
Warrantholder make a disposition of any of its rights to acquire Preferred Stock
or Preferred Stock issuable upon exercise of such rights unless and until (i) it
shall have notified the Company of the proposed disposition, and (ii) if
requested by the Company, it shall have furnished the Company with an opinion of
counsel (which counsel may either be inside or outside counsel to the
Warrantholder) satisfactory to the Company and its counsel to the effect that
(A) appropriate action necessary for compliance with the 1933 Act has been
taken, or (B) an exemption from the registration requirements of the 1933 Act is
available. Notwithstanding the foregoing, the restrictions imposed upon the
transferability of any of its rights to acquire Preferred Stock or

                                       8.
<PAGE>

Preferred Stock issuable on the exercise of such rights do not apply to
transfers from the beneficial owner of any of the aforementioned securities to
its nominee or from such nominee to its beneficial owner, and shall terminate as
to any particular share of Preferred Stock when (1) such security shall have
been effectively registered under the 1933 Act and sold by the holder thereof in
accordance with such registration or (2) such security shall have been sold
without registration in compliance with Rule 144 under the 1933 Act, or (3) a
letter shall have been issued to the Warrantholder at its request by the staff
of the SEC or a ruling shall have been issued to the Warrantholder at its
request by the SEC stating that no action shall be recommended by such staff or
taken by the SEC, as the case may be, if such security is transferred without
registration under the 1933 Act in accordance with the conditions set forth in
such letter or ruling and such letter or ruling specifies that no subsequent
restrictions on transfer are required. Whenever the restrictions imposed
hereunder shall terminate, as hereinabove provided, the Warrantholder or holder
of a share of Preferred Stock then outstanding as to which such restrictions
have terminated shall be entitled to receive from the Company, without expense
to such holder, one or more new certificates for the Warrant or for such shares
of Preferred Stock not bearing any restrictive legend.

     (d) Financial Risk.  The Warrantholder has such knowledge and experience in
financial and business matters as to be capable of evaluating the merits and
risks of its investment, and has the ability to bear the economic risks of its
investment

     (e) Risk of No Registration.  The Warrantholder understands that if the
Company does not register with the SEC pursuant to Section 12 of the 1933 Act,
or file reports pursuant to Section 15(d), of the Securities Exchange Act of
1934 (the "1934 Act"), or if a registration statement covering the securities
under the 1933 Act is not in effect when it desires to sell (i) the rights to
purchase Preferred Stock pursuant to this Warrant Agreement, or (ii) the
Preferred Stock issuable upon exercise of the right to purchase, it may be
required to hold such securities for an indefinite period.  The Warrantholder
also understands that any sale of its rights of the Warrantholder to purchase
Preferred Stock or Preferred Stock which might be made by it in reliance upon
Rule 144 under the 1933 Act may be made only in accordance with the terms and
conditions of that Rule.

11.  Transfers.

     Subject to the terms and conditions contained in Section 10 hereof, this
Warrant Agreement and all rights hereunder are transferable in whole or in part
by the Warrantholder and any successor transferee, provided, however, in no
event shall the number of transfers of the rights and interests in all of the
Warrants exceed three (3) transfers.  The transfer shall be recorded on the
books of the Company upon receipt by the Company of a notice of transfer in the
form attached hereto as Exhibit II (the "Transfer Notice"), at its principal
offices and the payment to the Company of all transfer taxes and other
governmental charges imposed on such transfer.  When this Warrant shall have
been so transferred pursuant to Section 11, the holder hereof may be treated by
the Company and all other persons dealing with this Warrant as the absolute
owner and holder hereof for any purpose and as the person entitled to exercise
the rights represented by this Warrant, or to the registration of transfer
hereof on the books of the Company; and until due presentment for registered
holders hereof as the owner and holder for all purposes, and the company shall
not be affected by notice to the contrary.

                                       9.
<PAGE>

12.  Miscellaneous.

     (a) Effective Date.  The provisions of this Warrant Agreement shall be
construed and shall be given effect in all respects as if it had been executed
and delivered by the Company on the date hereof.  This Warrant Agreement shall
be binding upon any successors or assigns of the Company.

     (b) Attorney's Fees.  In any litigation, arbitration or court proceeding
between the Company and the Warrantholder relating hereto, the prevailing party
shall be entitled to attorneys' fees and expenses and all costs of proceedings
incurred in enforcing this Warrant Agreement.

     (c) Governing Law. This Warrant Agreement shall be governed by and
construed for all purposes under and in accordance with the laws of the State of
Illinois.

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

     (e) Notices.  Any notice required or permitted hereunder shall be given in
writing and shall be deemed effectively given upon personal delivery, facsimile
transmission (provided that the original is sent by personal delivery or mail as
hereinafter set forth) or seven (7) days alter deposit in the United States
mail, by registered or certified mail, addressed (i) to the Warrantholder at 49
Tanglewood Road, Wellesley, MA 02481, attention: Gregory Stento and (ii) to the
Company at One Kendall Square, Building 600, Cambridge, Massachusetts 02139,
attention: President (and/or if by facsimile, (650) 825-2205) or at such other
address as any such party may subsequently designate by written notice to the
other party.

     (f) Remedies. In the event of any default hereunder, the non-defaulting
party may proceed to protect and enforce 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 default, and/or an action for specific performance for any
default where such non-defaulting party will not have an adequate remedy at law
and where damages will not be readily ascertainable. The Company expressly
agrees that it shall not oppose an application by the Warrantholder or any other
person entitled to the benefit of this Agreement requiring specific performance
of any or all provisions hereof or enjoining the Company from continuing to
commit any such breach of this Agreement

     (g) 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
actions as may be necessary or appropriate in order to protect the rights of the
Warrantholder against impairment.

     (h) Survival.  The representations, warranties, covenants and conditions of
the respective parties contained herein or made pursuant to this Warrant
Agreement shall survive the execution and delivery of this Warrant Agreement

                                      10.
<PAGE>

     (i) Severability.  In the event any one or more of the provisions of this
warrant Agreement shall for any reason be held invalid, illegal or
unenforceable, the remaining provisions of this warrant Agreement shall be
unimpaired, and the invalid, illegal or unenforceable provision shall be
replaced by a mutually acceptable valid, legal and enforceable provision, which
comes closest to the intention of the parties underlying the invalid, illegal or
unenforceable provision.

     (j) Amendments; Headings.  Any provision of this Warrant Agreement may be
amended by a written instrument signed by the Company and by the Warrantholder.
The headings in this Warrant Agreement are for purposes of reference only, and
shall not limit or otherwise affect any of the terms hereof.

     (k) Additional Documents.  The Company, upon execution of this warrant
Agreement, shall provide the Warrantholder with certified resolutions with
respect to the representations, warranties and covenants set forth in
subparagraphs (a) through (d), (f) and (g) of Section 9 above.  The Company
shall also supply such other documents as the Warrantholder may from time to
time reasonably request.

           [THE REMAINDER OF THIS PAGE WAS INTENTIONALLY LEFT BLANK]

                                      11.
<PAGE>

     In Witness Whereof, the parties hereto have caused this Warrant Agreement
to be executed by its officers thereunto duly authorized as of the Effective
Date.

                                   Company:       Exelixis Pharmaceuticals, Inc.

                                   By: /s/ George A. Scangos
                                      ------------------------------------------

                                   Title: President, CEO
                                         ---------------------------------------

                                   Warrantholder: Gregory Stento

                                   By: /s/ Gregory Stento
                                      ------------------------------------------

                                   Title:
                                         ---------------------------------------

                                      12.
<PAGE>

                                   EXHIBIT I

                              NOTICE OF EXERCISE

To:________________________

(1)  The undersigned Warrantholder hereby elects to purchase shares of the
     Series A Preferred Stock of Exelixis Pharmaceuticals, Inc., pursuant to
     the terms of the Warrant Agreement dated the 17th day of August, 1998 (the
     "Warrant Agreement") between Exelixis Pharmaceuticals, Inc. and the
     Warrantholder, and tenders herewith payment of the purchase price for such
     shares in full, together with all applicable transfer taxes, if any.

(2)  In exercising its rights to purchase the Preferred Stock of Exelixis
     Pharmaceuticals, Inc., the undersigned hereby confirms and acknowledges the
     investment representations and warranties made in Section 10 of the Warrant
     Agreement.

(3)  Please issue a certificate or certificates representing said shares of
     Series A Preferred Stock in the name of the undersigned or in such other
     name as is specified below.

____________________________
(Name)

____________________________
(Address)

Warrantholder:  Gregory Stento

By:_________________________

Title:______________________

Date:_______________________

                                      13.
<PAGE>

                          ACKNOWLEDGMENT OF EXERCISE

     The undersigned ____________________________, hereby acknowledges receipt
of the "Notice of Exercise" from Gregory Stento, to purchase _____ shares of the
Series A Preferred Stock of Exelixis Pharmaceuticals, Inc., pursuant to the
terms of the Warrant Agreement, and further acknowledges that ________________
shares remain subject to purchase under the terms of the Warrant Agreement.

                              Company:  Exelixls Pharmaceuticals, Inc.

                              By:_____________________________________

                              Title:__________________________________

                              Date:___________________________________

                                      14.
<PAGE>

                                  EXHIBIT II

                                TRANSFER NOTICE

(To transfer or assign the foregoing Warrant Agreement execute this form and
supply required information.  Do not use this form to purchase shares.)

     FOR VALUE RECEIVED, the foregoing Warrant Agreement and all rights
evidenced thereby are hereby transferred and assigned to

____________________________________________________
(Please Print)

whose address is____________________________________

____________________________________________________

     Dated__________________________________________

     Holder's Signature_____________________________

     Holder's Address_______________________________

     _______________________________________________

Signature Guaranteed:_______________________________

     NOTE:     The signature to this Transfer Notice must correspond with the
               name as it appears on the face of the Warrant Agreement, without
               alteration or enlargement or any change whatever. Officers of
               corporations and those acting in a fiduciary or other
               representative capacity should file proper evidence of authority
               to assign the foregoing Warrant Agreement

                                      15.

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