1

[PALMER & DODGE LLP LETTERHEAD]

                                                                     EXHIBIT 5.1

                                February 1, 2001

ArQule, Inc.
19 Presidential Way
Woburn, Massachusetts 01801

We are rendering this opinion in connection with the Registration Statement on
Form S-3 (the "Registration Statement") filed by ArQule, Inc. (the "Company")
with the Securities and Exchange Commission under the Securities Act of 1933, as
amended (the "Securities Act"), on or about the date hereof. The Registration
Statement relates to 3,106,622 shares of the Company's Common Stock, $.01 par
value per share, comprising of (i) 3,092,037 shares of Common Stock currently
outstanding (the "Shares") and (ii) 14,585 shares of Common Stock (the "Warrant
Shares") issuable upon exercise of warrants to purchase Common Stock (the
"Warrants"). We understand that the Shares and the Warrant Shares are to be
offered and sold in the manner described in the Registration Statement.

We have acted as your counsel in connection with the preparation of the
Registration Statement and are familiar with the proceedings taken by the
Company in connection with the authorization, issuance and sale of the Shares
and the Warrant to the selling stockholders. We have examined all such documents
as we consider necessary to enable us to render this opinion.

Based on the foregoing, we are of the opinion that upon the issuance and
delivery of the Shares to the selling stockholders, the Shares were validly
issued, fully paid, and nonassessable, and that upon exercise of the Warrants in
accordance with the terms thereof, the Warrant Shares will be validly issued,
fully paid and non-assessable.

We hereby consent to the filing of this opinion as an exhibit to the
Registration Statement and to the reference to our firm under the caption "Legal
Matters" in the prospectus filed as part thereof.


                                Very truly yours,

                                /s/ PALMER & DODGE LLP