<PAGE>   1
                                                                     EXHIBIT 4.3


No. CW-                               Right to Purchase                Shares of
                                      Common Stock of Axys Pharmaceuticals, Inc.

                                     COMPANY

                          COMMON STOCK PURCHASE WARRANT


              COMPANY, a Delaware corporation, hereby certifies that, for value
received, _________________ or registered assigns (the "Holder"), is entitled,
subject to the terms set forth below, to purchase from the Company at any time
or from time to time before 5:00 p.m., New York City time, on the Expiration
Date (such capitalized term and all other capitalized terms used herein having
the respective meanings provided herein), _________________ fully paid and
nonassessable shares of Common Stock at a purchase price per share equal to the
Purchase Price. The number of such shares of Common Stock and the Purchase Price
are subject to adjustment as provided in this Warrant.

              As used herein the following capitalized terms, unless the context
otherwise requires, have the following respective meanings:

              "Aggregate Purchase Price" means at any time an amount equal to
       the product obtained by multiplying (x) the Purchase Price times (y) the
       number of shares of Common Stock for which this Warrant may be exercised
       at such time.

              "AMEX" means the American Stock Exchange, Inc.

              "Business Day" means any day other than a Saturday, Sunday or
       other day on which commercial banks in The City of New York are
       authorized or required by law to remain closed.

              "Common Stock" includes the Company's Common Stock, par value
       $.001 per share, and the related Preferred Share Purchase Rights (and any
       similar rights issued with respect to the Common Stock) as authorized on
       the date hereof, and any other securities into which or for which the
       Common Stock or the related Preferred Share Purchase Rights (and any
       similar rights issued with respect to the Common Stock) may be converted
       or exchanged pursuant to a plan of recapitalization, reorganization,
       merger, sale of assets

<PAGE>   2

       or otherwise and any stock (other than Common Stock) and other securities
       of the Company or any other Person which the Holder at any time shall be
       entitled to receive, or shall have received, on the exercise of this
       Warrant, in lieu of or in addition to Common Stock.

              "Common Stock Equivalents" means any warrant, option, subscription
       or purchase right with respect to shares of Common Stock, any security
       convertible into, exchangeable for, or otherwise entitling the holder
       thereof to acquire, shares of Common Stock or any warrant, option,
       subscription or purchase right with respect to any such convertible,
       exchangeable or other security.

              "Common Stock Purchase Agreement" means the Common Stock Purchase
       Agreement, dated as of _________, by and between the Company _________, a
       ___________ corporation.

              "Company" shall include _______________, a __________ corporation,
       and any corporation that shall succeed to or assume the obligations of
       Axys Pharmaceuticals, Inc. hereunder in accordance with the terms hereof.

              "Current Fair Market Value" means when used with respect to the
       Common Stock as of a specified date with respect to each share of Common
       Stock, the average of the closing prices of the Common Stock sold on all
       securities exchanges (including the Nasdaq and the Nasdaq SmallCap) on
       which the Common Stock may at the time be listed, or, if there have been
       no sales on any such exchange on such day, the average of the highest bid
       and lowest asked prices on all such exchanges at the end of such day, or,
       if on such day the Common Stock is not so listed, the average of the
       representative bid and asked prices quoted in the NASDAQ System as of
       4:00 p.m., New York City time, or, if on such day the Common Stock is not
       quoted in the NASDAQ System, the average of the highest bid and lowest
       asked price on such day in the domestic over-the-counter market as
       reported by the National Quotation Bureau, Incorporated, or any similar
       successor organization, in each such case averaged over a period of ten
       Trading Days consisting of the day as of which the Current Fair Market
       Value of Common Stock is being determined (or if such day is not a
       Trading Day, the Trading Day next preceding such day) and the nine
       consecutive Trading Days prior to such day. If on the date for which
       Current Fair Market Value is to be determined 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 price per share which the Company could then obtain from a
       willing buyer (not an employee or director of the Company at the time of
       determination) in an arms'-length transaction for

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       shares of Common Stock sold by the Company, from authorized but unissued
       shares, as determined in good faith by the Board of Directors.

              "Expiration Date" means ____________.

              "Issuance Date" means the date of original issuance of this
       Warrant.

              "Market Price" means with respect to any security on any day the
       closing bid price of such security on such day on the Nasdaq, the Nasdaq
       SmallCap, the NYSE, or the AMEX, as applicable, or, if such security is
       not listed or admitted to trading on the Nasdaq, the NYSE or the AMEX, on
       the principal national securities exchange or quotation system on which
       such security is quoted or listed or admitted to trading, in any such
       case as reported by Bloomberg, L.P.

              "Nasdaq" means the Nasdaq National Market.

              "Nasdaq SmallCap" means the Nasdaq SmallCap Market.

              "1934 Act" means the Securities Exchange Act of 1934, as amended.

              "1933 Act" means the Securities Act of 1933, as amended.

              "Note Purchase Agreement" means the Note Purchase Agreement, dated
       as of ________, by and between the Company and the original Holder of
       this Warrant.

              "Notes" means any of the Note issued by the Company pursuant to
       the applicable Supplemental Indenture, the Note Purchase Agreement or any
       Other Note Purchase Agreements.

              "NYSE" means the New York Stock Exchange, Inc.

              "Other Note Purchase Agreements" means the several Note Purchase
       Agreements, dated as of the date of the Note Purchase Agreement, by and
       between the Company and the several buyers named therein.

              "Other Securities" means any stock (other than Common Stock) and
       other securities of the Company or any other Person which the Holder at
       any time shall be entitled to receive, or shall have received, on the
       exercise of this Warrant, in lieu of or in addition to Common Stock, or
       which at any time shall be issuable or shall have been issued in exchange
       for or in replacement of Common Stock or Other Securities pursuant to
       Section 4.

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              "Other Warrants" means the Common Stock Purchase Warrants (other
       than this Warrant) issued or issuable by the Company pursuant to the Note
       Purchase Agreement and the Other Note Purchase Agreements.

              "Person" means an individual, partnership, corporation, limited
       liability company, trust or unincorporated organization, or a government
       or a governmental agency or political subdivision.

              "Preferred Share Purchase Rights" means the Preferred Share
       Purchase Rights issued or issuable pursuant to the Rights Agreement (or
       any similar rights hereafter issued by the Company with respect to the
       Common Stock).

              "Purchase Price" means ____________.

              "Registration Statement" shall have the meaning provided in the
       Note Purchase Agreement.

              "Reorganization Event" shall have the meaning provided in the
       applicable Supplemental Indenture.

              "Repurchase Event" shall have the meaning to be provided or
       provided in the applicable Supplemental Indenture.

              "Restricted Securities" means securities that are not eligible for
       resale pursuant to Rule 144 under the 1933 Act (or any successor
       provision).

              "Rights Agreement" means the Rights Agreement, dated as of October
       8, 1998, between the Company and Computershare Investor Services LLC, as
       Rights Agent.

              "SEC" means the Securities and Exchange Commission.

              "SEC Effective Date" shall have the meaning provided in the Note
       Purchase Agreement.

              "Subsidiary" means any corporation or other entity of which a
       majority of the capital stock or other ownership interests having
       ordinary voting power to elect a majority of the board of directors or
       other persons performing similar functions are at the time directly or
       indirectly owned by the Company.

              "Supplemental Indenture" means the Supplemental Indenture, dated
       as of _________, between the Company and ______________, as Trustee.

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              "Tender Offer" means a tender offer, exchange offer or other offer
       by the Company to repurchase outstanding shares of its capital stock.

              "Trading Day" means a day on which the national securities
       exchange, the Nasdaq or the Nasdaq SmallCap which then constitutes the
       principal securities market for the Common Stock is open for general
       trading.

              1.     EXERCISE OF WARRANT.

              (a) EXERCISE. This Warrant may be exercised by the Holder in full
at any time or in part from time to time on or before the Expiration Date by (x)
surrendering this Warrant to the Company, (y) giving a subscription form in the
form of EXHIBIT 1 to this Warrant (duly executed by the Holder) to the Company,
and (z) making payment, in cash or by certified or official bank check payable
to the order of the Company, or by wire transfer of funds to the account of the
Company, in any such case, in the amount obtained by multiplying (a) the number
of shares of Common Stock designated by the Holder in the subscription form by
(b) the Purchase Price then in effect. On any partial exercise the Company will
forthwith issue and deliver to or upon the order of the Holder a new Warrant or
Warrants of like tenor, in the name of the Holder or as the Holder (upon payment
by the Holder of any applicable transfer taxes) may request, providing in the
aggregate on the face or faces thereof for the purchase of the number of shares
of Common Stock for which such Warrant or Warrants may still be exercised. The
subscription form may be surrendered by telephone line facsimile transmission to
such telephone number for the Company as shall have been specified in writing to
the Holder by the Company; provided, however, that if the subscription form is
given to the Company by telephone line facsimile transmission the Holder shall
send an original of such subscription form to the Company within ten Business
Days after such subscription form is so given to the Company; provided further,
however, that any failure or delay on the part of the Holder in giving such
original of any subscription form shall not affect the validity or the date on
which such subscription form is so given by telephone line facsimile
transmission. In connection with any exercise of this Warrant, the Holder shall
also furnish to the Company such other documentation as required by applicable
law and reasonably requested by the Company in writing.

              (b) NET EXERCISE. Notwithstanding anything to the contrary
contained in Section 1(a), the Holder may elect to exercise this Warrant, in
whole or in part, by receiving shares of Common Stock equal to the net issuance
value (as determined below) of this Warrant, or any part hereof, upon surrender
of the subscription form annexed hereto (duly executed by the Holder) to the
Company (followed by surrender of this Warrant to the Company within three
Trading Days after surrender of such subscription form), in which event the
Company shall issue

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to the Holder a number of shares of Common Stock computed using the following
formula:

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

where,

              X =    the number of shares of Common Stock to be issued to the
                     Holder

              Y =    the number of shares of Common Stock as to which this
                     Warrant is to be exercised

              A =    the Current Fair Market Value of one share of Common Stock
                     calculated as of the last Trading Day immediately preceding
                     the exercise of this Warrant

              B =    the Purchase Price

              2. DELIVERY OF STOCK CERTIFICATES, ETC., ON EXERCISE. As soon as
practicable after the exercise of this Warrant and in any event within three
Trading Days thereafter, upon the terms and subject to the conditions of this
Warrant, the Company at its expense (including the payment by it of any
applicable issue or stamp taxes) will cause to be issued in the name of and
delivered to the Holder, or as the Holder (upon payment by the Holder of any
applicable transfer taxes) may direct, a certificate or certificates for the
number of fully paid and nonassessable shares of Common Stock (or Other
Securities) to which the Holder shall be entitled on such exercise, in such
denominations as may be requested by the Holder, plus, in lieu of any fractional
share to which the Holder would otherwise be entitled, cash equal to such
fraction multiplied by the then Current Fair Market Value of one full share,
together with any other stock or other securities or any property (including
cash, where applicable) to which the Holder is entitled upon such exercise
pursuant to Section 1 or otherwise. Upon exercise of this Warrant as provided
herein, the Company's obligation to issue and deliver the certificates for
Common Stock shall be absolute and unconditional, irrespective of the absence of
any action by the Holder to enforce the same, any waiver or consent with respect
to any provision hereof, the recovery of any judgment against any Person or any
action to enforce the same, any failure or delay in the enforcement of any other
obligation of the Company to the Holder, or any setoff, counterclaim,
recoupment, limitation or termination, or any breach or alleged breach by the
Holder or any other Person of any obligation to the Company or any violation or
alleged violation of law by the Holder or any other Person, and irrespective of
any other circumstance which might otherwise limit such obligation of the
Company to the Holder in connection with

<PAGE>   7

such exercise. If the Company fails to issue and deliver the certificates for
the Common Stock to the Holder pursuant to the first sentence of this paragraph
as and when required to do so, in addition to any other liabilities the Company
may have hereunder and under applicable law, the Company shall pay or reimburse
the Holder on demand for all out-of-pocket expenses including, without
limitation, fees and expenses of legal counsel incurred by the Holder as a
result of such failure.

              3. ADJUSTMENT FOR DIVIDENDS IN OTHER STOCK, PROPERTY, ETC.;
RECLASSIFICATION, ETC. In case at any time or from time to time on or after the
Issuance Date, all the holders of Common Stock (or Other Securities) shall have
received, or (on or after the record date fixed for the determination of
stockholders eligible to receive) shall have become entitled to receive, without
payment therefor,

              (a) other or additional stock or other securities or property
       (other than cash) by way of dividend, or

              (b) any cash (excluding cash dividends payable solely out of
       earnings or earned surplus of the Company), or

              (c) other or additional stock or other securities or property
       (including cash) by way of spin-off, split-up, reclassification,
       recapitalization, combination of shares or similar corporate
       rearrangement,

other than (i) additional shares of Common Stock (or Other Securities) issued as
a stock dividend or in a stock-split (adjustments in respect of which are
provided for in Section 5) and (ii) rights or warrants to subscribe for Common
Stock at less than the Current Fair Market Value (adjustments in respect of
which are provided in Section 6), then and in each such case the Holder, on the
exercise hereof as provided in Section 1, shall be entitled to receive the
amount of stock and other securities and property (including cash in the cases
referred to in subdivisions (b) and (c) of this Section 3) which the Holder
would hold on the date of such exercise if on the date thereof the Holder had
been the holder of record of the number of shares of Common Stock called for on
the face of this Warrant and had thereafter, during the period from the date
thereof to and including the date of such exercise, retained such shares and all
such other or additional stock and other securities and property (including cash
in the case referred to in subdivisions (b) and (c) of this Section 3)
receivable by the Holder as aforesaid during such period, giving effect to all
adjustments called for during such period by Section 4.

              4. EXERCISE UPON A REORGANIZATION EVENT. In case of any
Reorganization Event the Company shall, as a condition precedent to the
consummation of the transactions constituting, or announced as, such
Reorganization Event, cause effective provisions to be made so that the Holder
shall have the right thereafter, by exercising this Warrant (in lieu of the
shares of

<PAGE>   8

Common Stock of the Company and Other Securities or property purchasable and
receivable upon exercise of the rights represented hereby immediately prior to
such transaction) to purchase the kind and amount of shares of stock and other
securities and property (including cash) receivable upon such Reorganization
Event by a holder of the number of shares of Common Stock that might have been
received upon exercise of this Warrant immediately prior to such Reorganization
Event. Any such provision shall include provisions for adjustments in respect of
such shares of stock and other securities and property that shall be as nearly
equivalent as may be practicable to the adjustments provided for in this
Warrant. The provisions of this Section 4 shall apply to successive
Reorganization Events.

              5. ADJUSTMENT FOR CERTAIN EXTRAORDINARY EVENTS. In the event that
on or after the Issuance Date the Company shall (i) issue additional shares of
the Common Stock as a dividend or other distribution on outstanding Common
Stock, (ii) subdivide or reclassify its outstanding shares of Common Stock, or
(iii) combine its outstanding shares of Common Stock into a smaller number of
shares of Common Stock, then, in each such event, the Purchase Price shall,
simultaneously with the happening of such event, be adjusted by multiplying the
Purchase Price in effect immediately prior to such event by a fraction, the
numerator of which shall be the number of shares of Common Stock outstanding
immediately prior to such event and the denominator of which shall be the number
of shares of Common Stock outstanding immediately after such event, and the
product so obtained shall thereafter be the Purchase Price then in effect. The
Purchase Price, as so adjusted, shall be readjusted in the same manner upon the
happening of any successive event or events described herein in this Section 5.
The Holder shall thereafter, on the exercise hereof as provided in Section 1, be
entitled to receive that number of shares of Common Stock determined by
multiplying the number of shares of Common Stock which would be issuable on such
exercise immediately prior to such issuance by a fraction of which (i) the
numerator is the Purchase Price in effect immediately prior to such issuance and
(ii) the denominator is the Purchase Price in effect on the date of such
exercise.

              6. ISSUANCE OF RIGHTS OR WARRANTS TO COMMON STOCKHOLDERS AT LESS
THAN CURRENT FAIR MARKET VALUE. In case the Company shall on or after the
Issuance Date issue rights or warrants to all holders of its outstanding shares
of Common Stock entitling them to subscribe for or purchase shares of Common
Stock at a price per share less than the Current Fair Market Value on the record
date fixed for the determination of stockholders entitled to receive such rights
or warrants, then

              (a) the Purchase Price shall be adjusted so that the same shall
       equal the price determined by multiplying the Purchase Price in effect at
       the opening of business on the day after such record date by a fraction
       of which the numerator shall be the number of shares of Common Stock
       outstanding

<PAGE>   9

       at the close of business on such record date plus the number of shares
       which the aggregate offering price of the total number of shares so
       offered would purchase at such Current Fair Market Value, and the
       denominator shall be the number of shares of Common Stock outstanding on
       the close of business on such record date plus the total number of
       additional shares of Common Stock so offered for subscription or
       purchase; and

              (b) the number of shares of Common Stock which the Holder may
       thereafter purchase upon exercise of this Warrant at the opening of
       business on the day after such record date shall be increased to a number
       equal to the quotient obtained by dividing (x) the Aggregate Purchase
       Price in effect immediately prior to such adjustment in the Purchase
       Price pursuant to clause (a) of this Section 6 by (y) the Purchase Price
       in effect immediately after such adjustment in the Purchase Price
       pursuant to clause (a) of this Section 6.

Such adjustment shall become effective immediately after the opening of business
on the day following the record date fixed for determination of stockholders
entitled to receive such rights or warrants. To the extent that shares of Common
Stock are not delivered pursuant to such rights or warrants, upon the expiration
or termination of such rights or warrants, the Purchase Price shall be
readjusted to the Purchase Price which would then be in effect had the
adjustments made upon the issuance of such rights or warrants been made on the
basis of delivery of only the number of shares of Common Stock actually
delivered and the number of shares of Common Stock for which this Warrant may
thereafter be exercised shall be readjusted (subject to proportionate adjustment
for any intervening exercises of this Warrant) to the number which would then be
in effect had the adjustments made upon the issuance of such rights or warrants
been made on the basis of delivery of only the number of shares of Common Stock
actually delivered. In the event that such rights or warrants are not so issued,
the Purchase Price shall again be adjusted to be the Purchase Price which would
then be in effect if such record date had not been fixed and the number of
shares of Common Stock for which this Warrant may thereafter be exercised shall
again be adjusted (subject to proportionate adjustment for any intervening
exercises of this Warrant) to be the number which would then be in effect if
such record date had not been fixed. In determining whether any rights or
warrants entitle the holder to subscribe for or purchase shares of Common Stock
at less than such Current Fair Market Value, and in determining the aggregate
offering price of such shares of Common Stock, there shall be taken into account
any consideration received for such rights or warrants, the value of such
consideration, if other than cash, to be determined by the Board of Directors.

              7. ISSUANCE AT LESS THAN CURRENT FAIR MARKET VALUE. (a) In case at
any time on or after the Issuance Date the Company shall issue shares of its

<PAGE>   10

Common Stock or Common Stock Equivalents (collectively, the "Newly Issued
Shares"), other than an issuance pro rata to all holders of its outstanding
Common Stock, at a price below the Current Fair Market Value of the Common Stock
at the time of such issuance, then following such issuance of Newly Issued
Shares the Purchase Price shall be reduced as provided in clause (b) of this
Section 7 and the number of shares of Common Stock which may be issued upon
exercise of this Warrant shall be increased as provided in clause (c) of this
Section 7.

              (b) The reduction in the Purchase Price following any such
adjustment shall be determined by multiplying the Purchase Price immediately
prior to such adjustment by a fraction, of which the numerator shall be the sum
of (1) the number of shares of Common Stock outstanding immediately prior to the
issuance of the Newly Issued Shares (calculated on a fully-diluted basis
assuming the exercise or conversion of all options, warrants, purchase rights or
convertible securities which are exercisable or convertible at the time of the
issuance of the Newly Issued Shares) plus (2) the number of shares of Common
Stock which the aggregate consideration, if any, received by the Company for the
number of Newly Issued Shares would purchase at a price equal to the Current
Fair Market Value of the Common Stock at the time of such issuance, and the
denominator shall be the sum of (X) the number of shares of Common Stock
outstanding immediately prior to the issuance of the Newly Issued Shares
(calculated on a fully-diluted basis assuming the exercise or conversion of all
options, warrants, purchase rights or convertible securities which are
exercisable or convertible at the time of the issuance of the Newly Issued
Shares) plus (Y) the number of Newly Issued Shares. The adjustment provided for
in this Section 7(b) may be expressed as the following mathematical formula:

<TABLE>
<S>                            <C>                         <C>
          ----------------------------------------------------------
                                    ( O +(C / FMV))         x PP
          ----------------------------------------------------------
                   NPP =               ( O + N )
          ----------------------------------------------------------
</TABLE>

where,

       C   =  aggregate consideration received by the Company for the Newly
              Issued Shares

       N   =  number of Newly Issued Shares

       O   =  number of shares of Common Stock outstanding (on a fully diluted
              basis, as described above) immediately prior to the issuance of
              the Newly Issued Shares

       FMV =  Current Fair Market Value of the Common Stock at the time of
              issuance of the Newly Issued Shares

<PAGE>   11

       PP  =  Purchase Price immediately prior to the issuance of the Newly
              Issued Shares

       NPP =  Purchase Price immediately after the issuance of the Newly Issued
              Shares

              (c) If the Purchase Price is reduced in connection with the
issuance of Newly Issued Shares as provided in Section 7(b), then the number of
shares of Common Stock for which this Warrant may thereafter be exercised shall
be increased at the time of such reduction in the Purchase Price to a number
equal to the quotient obtained by dividing (x) the Aggregate Purchase Price in
effect immediately prior to such issuance of Newly Issued Shares by (y) the
Purchase Price in effect immediately after such issuance of Newly Issued Shares
after giving effect to such reduction in the Purchase Price pursuant to Section
7(b).

              (d) Notwithstanding the foregoing, no adjustment shall be made
under this Section 7 by reason of:

              (1) the issuance by the Company of shares of Common Stock pro rata
to all holders of the Common Stock so long as (i) any adjustment required by
Section 5 is made and (ii) the Company shall have given notice thereof to the
Holder pursuant to Section 13;

              (2) the issuance by the Company of Newly Issued Shares in an
offering for cash for the account of the Company that is underwritten on a firm
commitment basis and (A) is registered under the 1933 Act or (B) sold in an
offering to "qualified institutional buyers" as defined in, and in a transaction
under, Rule 144A under the 1933 Act;

              (3) the issuance by the Company of shares of Common Stock upon
conversion of the Notes in accordance with the Supplemental Indenture or upon
exercise of this Warrant or the Other Warrants in accordance with the terms
hereof and thereof;

              (4) the issuance by the Company of shares of Common Stock in
payment of interest on the Notes in accordance with the terms thereof and the
Supplemental Indenture; and

              (5) the issuance of shares of Common Stock pursuant to the Common
Stock Purchase Agreement.

              8. EFFECT OF RECLASSIFICATION, CONSOLIDATION, MERGER OR SALE. (a)
If any of the following events occur, namely (i) any reclassification or change
of the outstanding shares of Common Stock (other than a change in par value, or
from

<PAGE>   12

par value to no par value, or from no par value to par value, or as a result of
a subdivision or combination), (ii) any consolidation, merger or combination of
the Company with another corporation as a result of which holders of Common
Stock shall be entitled to receive stock, securities or other property or assets
(including cash) with respect to or in exchange for such Common Stock, or (iii)
any sale or conveyance of the properties and assets of the Company as, or
substantially as, an entirety to any other Person as a result of which holders
of Common Stock shall be entitled to receive stock, securities or other property
or assets (including cash) with respect to or in exchange for such Common Stock,
then the Company or the successor or purchasing Person, as the case may be,
shall execute with the Holder a written agreement providing that (x) this
Warrant shall thereafter entitle the Holder to purchase the kind and amount of
shares of stock and other securities or property or assets (including cash)
receivable upon such reclassification, change, consolidation, merger,
combination, sale or conveyance by the holder of a number of shares of Common
Stock issuable upon exercise of this Warrant (assuming, for such purposes, a
sufficient number of authorized shares of Common Stock available to exercise
this Warrant) immediately prior to such reclassification, change, consolidation,
merger, combination, sale or conveyance assuming such holder of Common Stock did
not exercise such holder's rights of election, if any, as to the kind or amount
of securities, cash or other property receivable upon such consolidation,
merger, statutory exchange, sale or conveyance (provided that, if the kind or
amount of securities, cash or other property receivable upon such consolidation,
merger, statutory exchange, sale or conveyance is not the same for each share of
Common Stock in respect of which such rights of election shall not have been
exercised ("non-electing share"), then for the purposes of this Section 8 the
kind and amount of securities, cash or other property receivable upon such
consolidation, merger, statutory exchange, sale or conveyance for each
non-electing share shall be deemed to be the kind and amount so receivable per
share by a plurality of the non-electing shares), (y) in the case of any such
successor or purchasing Person, upon such consolidation, merger, combination,
sale or conveyance such successor or purchasing Person shall be jointly and
severally liable with the Company for the performance of all of the Company's
obligations under this Warrant and the Note Purchase Agreement and (z) if
registration or qualification is required under the 1933 Act or applicable state
law for this Warrant or the issuance to the Holder of the shares of such shares
of stock and other securities so issuable upon exercise of this Warrant, such
registration or qualification shall be completed prior to such reclassification,
change, consolidation, merger, combination or sale. Such written agreement shall
provide for adjustments which shall be as nearly equivalent as may be
practicable to the adjustments provided for in this Warrant. If, in the case of
any such reclassification, change, consolidation, merger, combination, sale or
conveyance, the stock or other securities and assets receivable thereupon by a
holder of shares of Common Stock includes shares of stock or other securities
and assets of a corporation other than the successor or purchasing corporation,
as the case may be, in such reclassification, change, consolidation, merger,
combination,

<PAGE>   13

sale or conveyance, then such written agreement shall also be executed by such
other corporation and shall contain such additional provisions to protect the
interests of the Holder as the Board of Directors shall reasonably consider
necessary by reason of the foregoing.

       (b) The above provisions of this Section 8 shall similarly apply to
successive reclassifications, changes, consolidations, mergers, combinations,
sales and conveyances.

       (c) If this Section 8 applies to any event or occurrence, Section 4 shall
not apply to such event or occurrence.

              9. TAX ADJUSTMENTS. The Company may make such reductions in the
Purchase Price, in addition to those required by Sections 3, 4, 5, 6 and 7, as
the Board of Directors considers to be advisable to avoid or diminish any income
tax to holders of Common Stock or rights to purchase Common Stock resulting from
any dividend or distribution of stock (or rights to acquire stock) or from any
event treated as such for income tax purposes.

              10. MINIMUM ADJUSTMENT. (a) No adjustment in the Purchase Price
(and no related adjustment in the number of shares of Common Stock which may
thereafter be purchased upon exercise of this Warrant) shall be required unless
such adjustment would require an increase or decrease of at least 1% in the
Purchase Price; provided, however, that any adjustments which by reason of this
Section 10 are not required to be made shall be carried forward and taken into
account in any subsequent adjustment. All such calculations under this Warrant
shall be made by the Company and shall be made to the nearest cent or to the
nearest one hundredth of a share, as the case may be.

              (b) No adjustment need be made for a change in the par value of
the Common Stock or from par value to no par value or from no par value to par
value.

              11. NOTICE OF ADJUSTMENTS. Whenever the Purchase Price is adjusted
as herein provided, the Company shall promptly, but in no event later than five
Trading Days thereafter, give a notice to the Holder setting forth the Purchase
Price and number of shares of Common Stock which may be purchased upon exercise
of this Warrant after such adjustment and setting forth a brief statement of the
facts requiring such adjustment but which such statement shall not include any
information which would be material non-public information for purposes of the
1934 Act. Failure to deliver such notice shall not affect the legality or
validity of any such adjustment.

              12. FURTHER ASSURANCES. The Company will take all action that may
be necessary or appropriate in order that the Company may validly and legally

<PAGE>   14

issue fully paid and nonassessable shares of stock, free from all taxes, liens
and charges with respect to the issue thereof, on the exercise of all or any
portion of this Warrant from time to time outstanding.

              13. NOTICE TO HOLDER PRIOR TO CERTAIN ACTIONS. In case on or after
the Issuance Date:

              (a) the Company shall declare a dividend (or any other
distribution) on its Common Stock (other than in cash out of retained earnings);
or

              (b) the Company shall authorize the granting to the holders of its
Common Stock of rights or warrants to subscribe for or purchase any share of any
class or any other rights or warrants; or

              (c) the Board of Directors shall authorize any reclassification of
the Common Stock (other than a subdivision or combination of its outstanding
Common Stock, or a change in par value, or from par value to no par value, or
from no par value to par value), or any consolidation or merger or other
business combination transaction to which the Company is a party and for which
approval of any stockholders of the Company is required, or the sale or transfer
of all or substantially all of the assets of the Company; or

              (d) there shall be pending the voluntary or involuntary
dissolution, liquidation or winding-up of the Company;

the Company shall give the Holder, as promptly as possible but in any event at
least ten Trading Days prior to the applicable date hereinafter specified, a
notice stating (x) the date on which a record is to be taken for the purpose of
such dividend, distribution or rights or warrants, or, if a record is not to be
taken, the date as of which the holders of Common Stock of record to be entitled
to such dividend, distribution or rights are to be determined, or (y) the date
on which such reclassification, consolidation, merger, other business
combination transaction, sale, transfer, dissolution, liquidation or winding-up
is expected to become effective or occur, and the date as of which it is
expected that holders of Common Stock of record who shall be entitled to
exchange their Common Stock for securities or other property deliverable upon
such reclassification, consolidation, merger, other business combination
transaction, sale, transfer, dissolution, liquidation or winding-up shall be
determined. Such notice shall not include any information which would be
material non-public information for purposes of the 1934 Act. Failure to give
such notice, or any defect therein, shall not affect the legality or validity of
such dividend, distribution, reclassification, consolidation, merger, sale,
transfer, dissolution, liquidation or winding-up. In the case of any such action
of which the Company gives such notice to the Holder or is required to give such
notice to the

<PAGE>   15

Holder, the Holder shall be entitled to give a subscription form to exercise
this Warrant in whole or in part that is contingent on the completion of such
action.

              14. RESERVATION OF STOCK, ETC., ISSUABLE ON EXERCISE OF WARRANTS.
The Company will at all times reserve and keep available out of its authorized
but unissued shares of capital stock, solely for issuance and delivery on the
exercise of this Warrant, a sufficient number of shares of Common Stock (or
Other Securities) to effect the full exercise of this Warrant and the exercise,
conversion or exchange of any other warrant or security of the Company
exercisable for, convertible into, exchangeable for or otherwise entitling the
holder to acquire shares of Common Stock (or Other Securities), and if at any
time the number of authorized but unissued shares of Common Stock (or Other
Securities) shall not be sufficient to effect such exercise, conversion or
exchange, the Company shall take such action as may be necessary to increase its
authorized but unissued shares of Common Stock (or Other Securities) to such
number as shall be sufficient for such purposes.

              15. TRANSFER OF WARRANT. This Warrant shall inure to the benefit
of the successors to and assigns of the Holder. This Warrant and all rights
hereunder, in whole or in part, are registrable at the office or agency of the
Company referred to below by the Holder in Person or by his duly authorized
attorney, upon surrender of this Warrant properly endorsed accompanied by an
assignment form in the form attached to this Warrant, or other customary form,
duly executed by the transferring Holder.

              16. REGISTER OF WARRANTS. The Company shall maintain, at the
principal office of the Company (or such other office as it may designate by
notice to the Holder), a register in which the Company shall record the name and
address of the Person in whose name this Warrant has been issued, as well as the
name and address of each successor and prior owner of such Warrant. The Company
shall be entitled to treat the Person in whose name this Warrant is so
registered as the sole and absolute owner of this Warrant for all purposes.

              17. EXCHANGE OF WARRANT. This Warrant is exchangeable, upon the
surrender hereof by the Holder at the office or agency of the Company referred
to in Section 15, for one or more new Warrants of like tenor representing in the
aggregate the right to subscribe for and purchase the number of shares of Common
Stock which may be subscribed for and purchased hereunder, each of such new
Warrants to represent the right to subscribe for and purchase such number of
shares as shall be designated by the Holder at the time of such surrender.

              18. REPLACEMENT OF WARRANT. On receipt by the Company of evidence
reasonably satisfactory to it of the ownership of and the loss, theft,
destruction or mutilation of this Warrant and (a) in the case of loss, theft or

<PAGE>   16

destruction, of indemnity from the Holder reasonably satisfactory in form to the
Company (and without the requirement to post any bond or other security), or (b)
in the case of mutilation, upon surrender and cancellation of this Warrant, the
Company will execute and deliver to the Holder a new Warrant of like tenor
without charge to the Holder.

              19. WARRANT AGENT. The Company may, by written notice to the
Holder, appoint the transfer agent and registrar for the Common Stock as the
Company's agent for the purpose of issuing Common Stock (or Other Securities) on
the exercise of this Warrant pursuant to Section 1, and the Company may, by
written notice to the Holder, appoint an agent having an office in the United
States of America for the purpose of exchanging this Warrant pursuant to Section
17, and replacing this Warrant pursuant to Section 18, or any of the foregoing,
and thereafter any such exchange or replacement, as the case may be, shall be
made at such office by such agent.

              20. REMEDIES. The Company stipulates that the remedies at law of
the Holder in the event of any default or threatened default by the Company in
the performance of or compliance with any of the terms of this Warrant are not
and will not be adequate, and that such terms may be specifically enforced by a
decree for the specific performance of any agreement contained herein or by an
injunction against a violation of any of the terms hereof or otherwise.

              21. NO RIGHTS OR LIABILITIES AS A STOCKHOLDER. This Warrant shall
not entitle the Holder to any voting rights or other rights as a stockholder of
the Company. Nothing contained in this Warrant shall be construed as conferring
upon Holder hereof the right to vote or to consent or to receive notice as a
stockholder of the Company on any matters or with respect to any rights
whatsoever as a stockholder of the Company. No dividends or interest shall be
payable or accrued in respect of this Warrant or the interest represented hereby
or the Common Stock (or Other Securities) purchasable hereunder until, and only
to the extent that, this Warrant shall have been exercised in accordance with
its terms.

              22. NOTICES, ETC. All notices and other communications from the
Company to the Holder shall be mailed by first class certified mail, postage
prepaid, at such address as may have been furnished to the Company in writing by
the Holder or at the address shown for the Holder on the register of Warrants
referred to in Section 16.

              23. AMENDMENT; WAIVER. This Warrant and any terms hereof may be
changed, waived, discharged or terminated only by an instrument in writing
signed by the party against which enforcement of such change, waiver, discharge
or termination is sought.

<PAGE>   17

              24. MISCELLANEOUS. This Warrant shall be construed and enforced in
accordance with and governed by the internal laws of the State of New York. The
headings, captions and footers in this Warrant are for purposes of reference
only, and shall not limit or otherwise affect any of the terms hereof. The
invalidity or unenforceability of any provision hereof shall in no way affect
the validity or enforceability of any other provision.

<PAGE>   18

              IN WITNESS WHEREOF, the Company has caused this Warrant to be duly
executed on its behalf by one of its officers thereunto duly authorized.

Dated:                           , 2000      AXYS PHARMACEUTICALS, INC.
      --------------------------



                                             By:
                                                --------------------------------
                                                Name:
                                                Title:

<PAGE>   19

                                   ASSIGNMENT

              For value received _________________________ hereby sell(s),
assign(s) and transfer(s) unto _________________________ (Please insert social
security or other Taxpayer Identification Number of assignee:
______________________________) the attached original, executed Warrant to
purchase _________________________ share of Common Stock of Axys
Pharmaceuticals, Inc., a Delaware corporation, and hereby irrevocably
constitutes and appoints _________________________ attorney to transfer the
Warrant on the books of the Company, with full power of substitution in the
premises.

              Capitalized terms used in this Assignment and not defined in this
Assignment shall have the respective meanings provided in the Warrant.



Dated:                                  NAME:
       ---------------------------           -----------------------------------


                                        ----------------------------------------
                                                      Signature(s)

<PAGE>   20

                                                                       EXHIBIT 1

                              FORM OF SUBSCRIPTION

                           AXYS PHARMACEUTICALS, INC.

                   (To be signed only on exercise of Warrant)

TO:    Axys Pharmaceuticals, Inc.
       180 Kimball Way
       South San Francisco, California 94080

       Attention:  Chief Financial Officer

       Facsimile No.: (650) _________

       1. The undersigned Holder of the attached original, executed Warrant
hereby elects to exercise its purchase right under such Warrant with respect to
______________ shares (the "Exercise Shares") of Common Stock, as defined in the
Warrant, of Axys Pharmaceuticals, Inc., a Delaware corporation (the "Company").

       2. The undersigned Holder (check one):

       -      (a) elects to pay the aggregate purchase price for such shares of
              Common Stock (i) in lawful money of the United States or by the
              enclosed certified or official bank check payable in United States
              dollars to the order of the Company in the amount of $___________,
              or (ii) by wire transfer of United States funds to the account of
              the Company in the amount of $____________, which transfer has
              been made before or simultaneously with the delivery of this Form
              of Subscription pursuant to the instructions of the Company;

              or

       -      (b) elects to receive shares of Common Stock having a value equal
              to the value of the Warrant calculated in accordance with Section
              1(b) of the Warrant.

       3. Please issue a stock certificate or certificates representing the
appropriate number of shares of Common Stock in the name of the undersigned or
in such other names as is specified below:

       Name:
            --------------------------------------------------------------------

<PAGE>   21

       Address:
               -----------------------------------------------------------------

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



Dated:
      -----------------------             --------------------------------------
                                            (Signature must conform to name of
                                          Holder as specified on the face of the
                                                         Warrant)

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

                                          --------------------------------------
(Address)