1
                                                                    EXHIBIT 5.1

                        [LETTERHEAD OF LATHAM & WATKINS]


                                  July 10, 2000




Axys Pharmaceuticals, Inc.
180 Kimball Way
South San Francisco, CA  94080

              Re:    $35,000,000 Aggregate Offering of Debt Securities and
                     Warrants of Axys Pharmaceuticals, Inc.

Ladies and Gentlemen:

              In connection with the Registration Statement on Form S-3
(Registration No. 333-35828) filed by Axys Pharmaceuticals, Inc., a Delaware
corporation (the "Company"), on April 28, 2000 with the Securities and Exchange
Commission (the "Commission") under the Securities Act of 1933, as amended (the
"Securities Act"), as amended by Post-Effective Amendment No. 1 thereto filed
with the Commission on May 22, 2000 (as so amended, the "Registration
Statement"), you have requested our opinion with respect to the matters set
forth below.

              You have provided us with a base prospectus (the "Prospectus")
which is a part of the Registration Statement. The Prospectus provides that it
will be supplemented in the future by one or more supplements to the Prospectus
(each a "Prospectus Supplement"). The Prospectus as supplemented by various
Prospectus Supplements will provide for the issuance and sale by the Company of
up to $35,000,000 aggregate offering price of (i) one or more series of the
Company's debt securities (the "Debt Securities") or (ii) warrants (the
"Warrants") to purchase shares of the Company's common stock, par value $.001
per share (the "Common Stock"). Any Debt Securities may be exchangeable and/or
convertible into shares of Common Stock. In addition, shares of Common Stock may
be issued in payment of interest with respect to a particular issuance of Debt
Securities. The Debt Securities and Warrants are collectively referred to herein
as the "Securities." The Debt Securities may be issued pursuant to one or more
indentures and one or more supplements thereto (collectively, the "Indentures"),
in each case between the Company and a trustee (each, a "Trustee").

   2

Axys Pharmaceuticals, Inc.
July 10, 2000
Page 2

              In our capacity as your special counsel in connection with the
Registration Statement, we are generally familiar with the proceedings taken and
proposed to be taken by the Company in connection with the authorization and
issuance of the Securities. For purposes of this opinion, we have assumed that
such proceedings will be timely and properly completed, in accordance with all
requirements of applicable federal, Delaware and New York laws, in the manner
presently proposed.

              We have made such legal and factual examinations and inquiries,
including an examination of originals and copies certified or otherwise
identified to our satisfaction, of all such documents, corporate records and
instruments of the Company as we have deemed necessary or appropriate for
purposes of this opinion. In our examination, we have assumed the genuineness of
all signatures, the authenticity of all documents submitted to us as originals,
and the conformity to authentic original documents of all documents submitted to
us as copies.

              We have been furnished with, and with your consent have
exclusively relied upon, certificates of officers of the Company with respect to
certain factual matters. In addition, we have obtained and relied upon such
certificates and assurances from public officials as we have deemed necessary.

              We are opining herein as to the effect on the subject transaction
only of the federal securities laws of the United States, the General
Corporation Law of the State of Delaware and the internal laws of the State of
New York, and we express no opinion with respect to the applicability thereto,
or the effect thereon, of the laws of any other jurisdiction or, in the case of
Delaware, any other laws, or as to any matters of municipal law or the laws of
any local agencies within any state.

              Subject to the foregoing and the other qualifications set forth
herein, it is our opinion that, as of the date hereof:

              1. When (a) the Debt Securities have been duly established in
accordance with the terms of the applicable Indentures (including, without
limitation, the adoption by the Board of Directors of the Company of a
resolution duly authorizing the issuance and delivery of the Securities), duly
authenticated by the Trustee and duly executed and delivered on behalf of the
Company against payment therefor in accordance with the terms and provisions of
the applicable Indenture and as contemplated by the Registration Statement, the
Prospectus and the related Prospectus Supplement(s), and (b) the Warrants have
been duly established, authorized and approved by the Board of Directors of the
Company and duly executed and delivered on behalf of the Company against payment
therefor in accordance with the terms and provisions thereof and as contemplated
by the Registration Statement, the Prospectus and the related Prospectus
Supplement(s), and (c) when the Registration Statement and any required
post-effective amendment thereto have all become and remain effective under the
Securities Act, and (d) assuming that the terms of the Securities as executed
and delivered are as described in the Registration Statement, the Prospectus and
the related Prospectus Supplement(s), and (e)

   3

Axys Pharmaceuticals, Inc.
July 10, 2000
Page 3

assuming that the Securities as executed and delivered do not violate any law
applicable to the Company or result in a default under or breach of any
agreement or instrument binding upon the Company, and (f) assuming that the
Securities as executed and delivered comply with all requirements and
restrictions, if any, applicable to the Company, whether imposed by any court or
governmental or regulatory body having jurisdiction over the Company, and (g)
assuming that the Securities are then issued and sold as contemplated in the
Registration Statement, the Prospectus and the related Prospectus Supplement(s),
the Securities will constitute valid and legally binding obligations of the
Company, enforceable against the Company in accordance with the terms of the
Securities.

              2. The Company has the authority pursuant to its Certificate of
Incorporation to issue up to 50,000,000 shares of Common Stock. Upon adoption by
the Board of Directors of the Company of a resolution in form and content as
required by applicable law and upon issuance and delivery of and payment for
such shares in the manner contemplated by the Registration Statement, the
Prospectus and the related Prospectus Supplement(s) and by such resolution, (a)
such shares of Common Stock duly issued upon the exchange or conversion of Debt
Securities, if any, that are exchangeable or convertible into Common Stock, (b)
such shares of Common Stock issued in payment of interest with respect to a
particular issuance of Debt Securities, if any, in accordance with the terms
thereof and (c) such shares of Common Stock issued upon due exercise of Warrants
against payment in full of the exercise price therefor, will be validly issued,
fully paid and nonassessable.

              The opinion set forth in paragraph 1 above is subject to the
following exceptions, limitations and qualifications: (i) the effect of
bankruptcy, insolvency, reorganization, moratorium or other similar laws now or
hereafter in effect relating to or affecting the rights and remedies of
creditors; (ii) the effect of general principles of equity, including without
limitation, concepts of materiality, reasonableness, good faith and fair dealing
and the possible unavailability of specific performance or injunctive relief,
regardless of whether enforcement is considered in a proceeding in equity or at
law, and the discretion of the court before which any proceeding therefor may be
brought; (iii) the unenforceability of any waiver of rights or defenses with
respect to stay, extension or usury laws; and (v) we express no opinion with
respect to whether acceleration of the Debt Securities may affect the
collectibility of any portion of the stated principal amount thereof which might
be determined to constitute unearned interest thereon.


              We assume for purposes of the opinion set forth in paragraph 2
above the correctness and due completion of the matters set forth in clauses
(a) through (g) of paragraph 1 above.

              We assume for purposes of this opinion that the Company has been
duly incorporated and is validly existing as a corporation under the laws of the
State of Delaware and has the corporate power and authority to issue and sell
the Securities and the Common Stock; that the applicable Indenture has been duly
authorized by all necessary corporate action by the Company, has been duly
executed and delivered by the Company and constitutes the legally valid, binding
and enforceable obligation of the Company enforceable against the Company in
accordance with its terms; and the Trustee for each Indenture is duly organized,
validly existing and

   4

Axys Pharmaceuticals, Inc.
July 10, 2000
Page 4

in good standing under the laws of its jurisdiction of organization; that the
Indenture constitutes a legally valid, binding and enforceable obligation of the
Trustee, enforceable against the Trustee in accordance with its terms; and that
the Trustee is in compliance, generally and with respect to acting as Trustee
under the applicable Indenture, with all applicable laws and regulations; and
that the Trustee has the requisite organizational and legal power and authority
to perform its obligations under the applicable Indenture.

              We consent to your filing this opinion as an exhibit to the
Registration Statement and to the reference to our firm under the caption "Legal
Matters" in the Prospectus included therein.

                                   Very truly yours,


                                   /s/ Latham & Watkins