13G Filing: Biotechnology Value Fund LP and Arqule Inc (ARQL)

 UNITED STATES

SECURITIES AND EXCHANGE
COMMISSION

Washington, D.C. 20549

SCHEDULE 13G

(Rule 13d-102)

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT

TO RULES 13d-1(b), (c),
AND (d) AND AMENDMENTS THERETO FILED

PURSUANT TO RULE 13d-2(b)

(Amendment No. 6)¹

Check the appropriate box
to designate the rule pursuant to which this Schedule is filed:

This amendment corrects a typographical error
made to the previous 13G amendment regarding the number of shares acquired.

ArQule, Inc., a Delaware corporation (the “Issuer”).

One Wall Street

Burlington, Massachusetts 01803

Biotechnology Value Fund, L.P. (“BVF”)

1 Sansome Street, 30^th Floor

San Francisco, California 94104

Citizenship: Delaware

Biotechnology Value Fund II, L.P. (“BVF2”)

1 Sansome Street, 30^th Floor

San Francisco, California 94104

Citizenship: Delaware

Biotechnology Value Trading Fund OS
LP (“Trading Fund OS”)

PO Box 309 Ugland House

Grand Cayman, KY1-1104

Cayman Islands

Citizenship: Cayman Islands

BVF Partners OS Ltd. (“Partners
OS”)

PO Box 309 Ugland House

Grand Cayman, KY1-1104

Cayman Islands

Citizenship: Cayman Islands

BVF Partners L.P. (“Partners”)

1 Sansome Street, 30th Floor

San Francisco, California 94104

Citizenship: Delaware

BVF Inc.

1 Sansome Street, 30^th Floor

San Francisco, California 94104

Citizenship: Delaware

Mark N. Lampert (“Mr. Lampert”)

1 Sansome Street, 30^th Floor

San Francisco, California 94104

Citizenship: United States

Each of the foregoing is referred to
as a “Reporting Person” and collectively as the “Reporting Persons.”

Common Stock, par value $0.01 per share (the “Common
Stock”)

04269E107

On October 11, 2017, the Reporting
Persons participated in a private placement (the “Private Placement”) with the Issuer. Pursuant to the Private Placement,
the Reporting Persons acquired in the aggregate 9,037,054 Shares of Common Stock and warrants (the “Warrants”) exercisable
for an aggregate of 2,439,932 Shares of Common Stock. Pursuant to the Private Placement, the Warrants are subject to an exercise
limitation, and may not be exercised if, after such exercise, the Reporting Persons would beneficially own in the aggregate, as
determined in accordance with Section 13(d) of the Securities Exchange Act of 1934, more than 19.9% of the number of shares of
Common Stock then issued and outstanding. Such Warrants have an initial exercise price of $1.75 per Share, subject to adjustment
pursuant to the terms of the Warrants, and expire on October 11, 2021. As of October 16, 2017, the warrant exercise limitation
described in the prior sentence limits the aggregate exercise of the Warrants by the Reporting Persons to 1,116,177 out of the
2,439,932 shares of Common Stock underlying the Warrants owned by the Reporting Persons in the aggregate. In providing beneficial
ownership described herein, the Reporting Persons have assumed 1,116,177 of the 1,201,053 warrants owned by BVF would be exercised.
BVF2 holds warrants to purchase 823,231 additional shares which are excluded herein as a result of the 19.9% limitation. BVTOS
holds warrants to purchase 199,687 additional shares which are excluded herein as a result of the 19.9% limitation. The Reporting
Persons through certain managed accounts holds warrants to purchase 215,961 additional shares which are excluded herein as a result
of the 19.9% limitation.

As of October 16, 2017 (i) BVF beneficially
owned 8,821,008 shares of Common Stock, including 1,116,177 shares of Common Stock issuable upon the exercise of certain Warrants,
(ii) BVF2 beneficially owned 5,124,370 shares of Common Stock, and (iii) Trading Fund OS beneficially owned 1,378,710 shares of
Common Stock.

Partners OS as the general partner
of Trading Fund OS may be deemed to beneficially own the 1,378,710 shares of Common Stock beneficially owned by Trading Fund OS.

Partners, as the general partner of
BVF, BVF2, the investment manager of Trading Fund OS, and the sole member of Partners OS, may be deemed to beneficially own the
17,553,089 shares of Common Stock beneficially owned in the aggregate by BVF, BVF2, Trading Fund OS, and certain Partners managed
accounts (the “Partners Managed Accounts”), including 2,229,001 shares of Common Stock held in the Partners Managed
Accounts.

BVF Inc., as the general partner of
Partners, may be deemed to beneficially own the 17,553,089 shares of Common Stock beneficially owned by Partners.

Mr. Lampert, as a director and officer
of BVF Inc., may be deemed to beneficially own the 17,553,089 shares of Common Stock beneficially owned by BVF Inc.

The foregoing should not be construed
in and of itself as an admission by any Reporting Person as to beneficial ownership of any shares of Common Stock owned by another
Reporting Person. Partners OS disclaims beneficial ownership of the shares of Common Stock beneficially owned by Trading Fund OS.
Each of Partners, BVF Inc. and Mr. Lampert disclaims beneficial ownership of the shares of Common Stock beneficially owned by BVF,
BVF2, Trading Fund OS, and the Partners Managed Accounts, and the filing of this statement shall not be construed as an admission
that any such person or entity is the beneficial owner of any such securities.

The following percentages are based
on a denominator which is the sum of: (i) 71,171,551 shares of Common Stock outstanding as of July 20, 2017, as disclosed in the
Issuer’s Quarterly Report filed on Form 10-Q with the Securities and Exchange Commission on August 4, 2017, (ii) the 15,918,751
Shares of Common Stock issued by the Issuer pursuant to the Private Placement and (ii) certain of the 2,439,932 shares of Common
Stock underlying certain Warrants, as applicable.

As of October 16, 2017 (i) BVF beneficially
owned approximately 10.0% of the outstanding shares of Common Stock, including shares of Common Stock issuable upon the exercise
of certain Warrants, (ii) BVF2 beneficially owned approximately 5.8% of the outstanding shares of Common Stock, including shares
of Common Stock issuable upon the exercise of certain Warrants, (iii) Trading Fund OS beneficially owned approximately 1.6% of
the outstanding shares of Common Stock, (iv) Partners OS may be deemed to beneficially own approximately 1.6% of the outstanding
shares of Common Stock, and (v) each of Partners, BVF Inc. and Mr. Lampert may be deemed to beneficially own approximately 19.9%
of the outstanding shares of Common Stock (approximately 2.5% of which is held in the Partners Managed Accounts).

See Cover Pages Items 5-9.

See Cover Pages Items 5-9.

See Cover Pages Items 5-9.

See Cover Pages Items 5-9.

Not Applicable.

Partners, BVF Inc. and Mr. Lampert
share voting and dispositive power over the shares of Common Stock beneficially owned by BVF, BVF2, Trading Fund OS, and the Partners
Managed Accounts.

Not Applicable.

See Exhibit 99.1 to Amendment No. 3
to the Schedule 13G filed with the Securities and Exchange Commission on February 16, 2016.

Not Applicable.

By signing below each of
the undersigned certifies that, to the best of its knowledge and belief, the securities referred to above were not acquired and
are not held for the purpose of or with the effect of changing or influencing the control of the issuer of the securities and were
not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect.

SIGNATURE

After reasonable inquiry
and to the best of his knowledge and belief, each of the undersigned certifies that the information set forth in this statement
is true, complete and correct.

Dated: October 20, 2017