13G Filing: Baker Bros. Advisors and Anacor Pharmaceuticals, Inc. (ANAC)

SCHEDULE 13G

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549

Under
the Securities Exchange Act of 1934

(Amendment
No. 2)*

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

x
Rule 13d-1(b)

¨
Rule 13d-1(c)

¨
Rule 13d-1(d)

*The remainder
of this cover page shall be filled out for a reporting person’s initial filing on this form with respect to the subject class
of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover
page.

The information
required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of
the Securities Exchange Act of 1934 (the “Act”) or otherwise subject to the liabilities of that section of the Act,
but shall be subject to all other provisions of the Act (however, see the Notes).

CUSIP No.  032420101

CUSIP No.  032420101

CUSIP No.  032420101

CUSIP No.  032420101

Amendment No. 2 to Schedule 13G

This Amendment No. 2 to Schedule 13G amends and supplements
the previously filed Schedules 13G filed by Baker Bros. Advisors LP (the “Adviser”). Baker Bros. Advisors (GP) LLC
(the “Adviser GP”), Julian C. Baker and Felix J. Baker. Except as supplemented herein, such statements, as heretofore
amended and supplemented, remain in full force and effect.

(a) ¨
Broker or dealer registered under Section 15 of the Exchange Act.

(b) ¨
Bank as defined in section 3(a)(6) of the Exchange Act.

(c) ¨
Insurance company as defined in section 3(a)(19) of the Exchange Act.

(d) ¨
Investment company registered under section 8 of the Investment Company Act of 1940.

(e) x
An investment adviser in accordance with Rule 13d-1(b)(1)(ii)(E).

(f) ¨
An employee benefit plan or endowment fund in accordance with Rule 13d-1(b)(1)(ii)(F).

(g) x
A parent holding company or control person in accordance with Rule 13d-1(b)(1)(ii)(G).

(h) ¨
A savings association as defined in Section 3(b) of the Federal Deposit Insurance Act.

(i) ¨
A church plan that is excluded from the definition of an investment company under section 3(c)(14) of the Investment Company Act
of 1940.

(j) ¨
Group, in accordance with Rule 13d-1(b)(1)(ii)(J).

Items 5 through 9 and 11 of each of the cover pages to this
Amendment No. 2 are incorporated herein reference. Set forth below is the aggregate number of shares of Common Stock the Issuer
directly held by each of Baker Brothers Life Sciences, L.P. (“Life Sciences”), 14159, L.P. (“14159”), and
667, L.P. (“667”, and together with Life Sciences and 14159, the “Funds”) and the percentage of the Issuer’s
outstanding shares of Common Stock such holdings represent. The information set forth below is based upon 44,123,977 shares of
Common Stock outstanding as of October 30, 2015, as reported on the Issuer’s Form 10-Q filed with the SEC on November 6,
2015. Such percentage figures are calculated in accordance with Rule 13d-3 under the Securities Exchange Act of 1934, as amended.

Pursuant to the amended and restated management agreements,
among the Adviser, the Funds and their respective general partners, the Adviser has complete and unlimited discretion and authority
with respect to the Funds’ investments and voting power over investments.

The Adviser GP, Felix J. Baker and Julian C. Baker as principals
of the Adviser GP, and the Adviser may be deemed to be beneficial owners of securities of the Issuer directly held by the Funds,
and may be deemed to have the power to vote or direct the vote of and the power to dispose or direct the disposition of such securities.

The Reporting Persons disclaim beneficial ownership of the securities
held by each of the Funds, and this Amendment No. 2 shall not be deemed an admission that the Reporting Persons are the beneficial
owners of such securities for purposes of Section 13(d) or for any other purpose.

    If this statement is being
filed to report the fact that as of the date hereof the reporting person has ceased to be the beneficial owner of more than five
percent of the class of securities, check the following ¨. N/A

By signing below I certify that, to the best of my knowledge
and belief, the securities referred to above were acquired and are held in the ordinary course of business and 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 my knowledge and
belief, I certify that the information set forth in this statement is true, complete and correct.

February 10,
2016