SC 13D/A 1 tm218648d1_sc13da.htm SCHEDULE 13D/A

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549

SCHEDULE 13D

(Rule 13d-102)

INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT

TO RULE 13d-l(a) AND AMENDMENTS THERETO FILED PURSUANT

TO RULE 13d-2(a)

(Amendment No. 5)*

Kodiak Sciences Inc.

(Name of Issuer)

Common stock, par value $0.0001 per share

(Title of Class of Securities)

50015M109

(CUSIP number)

Alexandra A. Toohey

Chief Financial Officer

Baker Bros. Advisors LP

860 Washington Street, 3^rd Floor

New York, NY 10014

(212) 339-5690

(Name, address and telephone number of person authorized to receive notices and communications)

March 1, 2021

(Date of event which requires filing of this statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of Rule 13d-1(e), 13d-1(f) or 13d-1(g), check the following box ¨.

(Continued on the following pages)

(Page 1 of 9 Pages)

*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 or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act.

CUSIP No. 50015M109

Page 2 of 9 Pages

NAMES OF REPORTING PERSONS

Baker Bros. Advisors LP

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*

(a) ¨

(b) ¨

SEC USE ONLY

SOURCE OF FUNDS*

CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) or 2(e) o

CITIZENSHIP OR PLACE OF ORGANIZATION

Delaware

NUMBER OF

BENEFICIALLY

OWNED BY EACH

REPORTING

PERSON WITH

SOLE VOTING POWER: 14,054,698 (1)

SHARED VOTING POWER: 0

SOLE DISPOSITIVE POWER: 14,054,698 (1)

10.

SHARED DISPOSITIVE POWER: 0

11.

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON: 14,054,698 (1)

12.

CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES* ¨

13.

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

27.4% (1)(2)

14.

TYPE OF REPORTING PERSON*

IA, PN

(1) Includes 149,999 shares of common stock (“Common Stock”) of Kodiak Sciences Inc. (the “Issuer”) underlying 149,999 warrants that have an exercise price of $0.01 and expire on August 11, 2022 (“2022 Warrants”) and 24,747 shares of Common Stock underlying 24,747 non-qualified options exercisable for Common Stock (“Stock Options”).

(2) Based on 51,162,424 shares of Common Stock outstanding as of February 19, 2021 as reported in the Issuer’s Form 10-K filed with the Securities and Exchange Commission (“SEC”) on March 1, 2021.

CUSIP No. 50015M109

Page 3 of 9 Pages

NAMES OF REPORTING PERSONS

Baker Bros. Advisors (GP) LLC

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*

(a) ¨

(b) ¨

SEC USE ONLY

SOURCE OF FUNDS*

CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) or 2(e) o

CITIZENSHIP OR PLACE OF ORGANIZATION

Delaware

NUMBER OF

BENEFICIALLY

OWNED BY EACH

REPORTING

PERSON WITH

SOLE VOTING POWER: 14,054,698 (1)

SHARED VOTING POWER: 0

SOLE DISPOSITIVE POWER: 14,054,698 (1)

10.

SHARED DISPOSITIVE POWER: 0

11.

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON: 14,054,698 (1)

12.

CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES* ¨

13.

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

27.4% (1)(2)

14.

TYPE OF REPORTING PERSON*

HC, OO

(1) Includes 149,999 shares of Common Stock underlying 149,999 2022 Warrants and 24,747 shares of Common Stock underlying 24,747 Stock Options.

(2) Based on 51,162,424 shares of Common Stock outstanding as of February 19, 2021 as reported in the Issuer’s Form 10-K filed with the SEC on March 1, 2021.

CUSIP No. 50015M109

Page 4 of 9 Pages

NAMES OF REPORTING PERSONS

Felix J. Baker

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*

(a) ¨

(b) ¨

SEC USE ONLY

SOURCE OF FUNDS*

CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) or 2(e) o

CITIZENSHIP OR PLACE OF ORGANIZATION

United States

NUMBER OF

BENEFICIALLY

OWNED BY EACH

REPORTING

PERSON WITH

SOLE VOTING POWER: 14,054,698 (1)

SHARED VOTING POWER: 0

SOLE DISPOSITIVE POWER: 14,054,698 (1)

10.

SHARED DISPOSITIVE POWER: 0

11.

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON: 14,054,698 (1)

12.

CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES* ¨

13.

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

27.4% (1)(2)

14.

TYPE OF REPORTING PERSON*

IN, HC

(1) Includes 149,999 shares of Common Stock underlying 149,999 2022 Warrants and 24,747 shares of Common Stock underlying 24,747 Stock Options.

(2) Based on 51,162,424 shares of Common Stock outstanding as of February 19, 2021 as reported in the Issuer’s Form 10-K filed with the SEC on March 1, 2021.

CUSIP No 50015M109

Page 5 of 9 Pages

NAMES OF REPORTING PERSONS

Julian C. Baker

CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*

(a) ¨

(b) ¨

SEC USE ONLY

SOURCE OF FUNDS*

CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) or 2(e) ¨

CITIZENSHIP OR PLACE OF ORGANIZATION

United States

NUMBER OF

BENEFICIALLY

OWNED BY EACH

REPORTING

PERSON WITH

SOLE VOTING POWER: 14,054,698 (1)

SHARED VOTING POWER: 0

SOLE DISPOSITIVE POWER: 14,054,698 (1)

10.

SHARED DISPOSITIVE POWER: 0

11.

AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON: 14,054,698 (1)

12.

CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES* ¨

13.

PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

27.4% (1)(2)

14.

TYPE OF REPORTING PERSON*

IN, HC

(1) Includes 149,999 shares of Common Stock underlying 149,999 2022 Warrants and 24,747 shares of Common Stock underlying 24,747 Stock Options.

(2) Based on 51,162,424 shares of Common Stock outstanding as of February 19, 2021 as reported in the Issuer’s Form 10-K filed with the SEC on March 1, 2021.

Amendment No. 5 to Schedule 13D

This Amendment No. 5 to Schedule 13D amends and supplements the previously filed Schedules 13D filed by Baker Bros. Advisors LP (the “Adviser”), Baker Bros. Advisors (GP) LLC (the “Adviser GP”), Julian C. Baker and Felix J. Baker (collectively the “Reporting Persons”). Except as supplemented herein, such statements, as heretofore amended and supplemented, remain in full force and effect.

The Adviser GP is the sole general partner of the Adviser. Pursuant to the management agreements, as amended, among the Adviser, Baker Brothers Life Sciences, L.P. (“Life Sciences”) and 667, L.P. (“667”, and together with Life Sciences, the “Funds”), and their respective general partners, the Funds’ respective general partners relinquished to the Adviser all discretion and authority with respect to the investment and voting power over securities held by the Funds, and thus the Adviser has complete and unlimited discretion and authority with respect to the Funds’ investments and voting power over investments.

All capitalized terms contained herein but not otherwise defined shall have the meanings ascribed to such terms in the Schedule 13D, as amended. Information given in response to each item shall be deemed incorporated by reference in all other items, as applicable.

ITEM 5.

Interest in Securities of the Issuer.

Item 5 of this Schedule 13D is hereby amended and restated in its entirety as follows:

(a) and (b) Items 7 through 11 and 13 of each of the cover pages of this Amendment No. 5 are incorporated herein by reference.

Set forth below is the aggregate number of shares of common stock (“Common Stock”) of Kodiak Sciences Inc. (the “Issuer”), directly held by each of the Funds, which may be deemed to be indirectly beneficially owned by the Reporting Persons, as well as the shares of Common Stock that may be acquired upon exercise of warrants to purchase Common Stock at an exercise price of $0.01 per share that have an expiration date of August 11, 2022 (the “2022 Warrants”).

Holder	Common Stock		2022 Warrants
667, L.P.		1,143,396		11,184
Baker Brothers Life Sciences, L.P.		12,736,556		138,815
Total		13,879,952		149,999

The Adviser GP, Felix J. Baker and Julian C. Baker as managing members of the Adviser GP, and the Adviser may be deemed to be beneficial owners of securities of the Issuer directly held by the Funds.

Felix J. Baker, a managing member of the Adviser GP, currently serves on the Issuer’s Board of Directors (the “Board”). He is Chair of the Compensation Committee and serves on the Nominating/Governance Committee. Felix J. Baker, as compensation for his service on the Board, receives non-qualified stock options to purchase shares of Common Stock of the Issuer (“Stock Options”). Felix J. Baker holds 24,747 vested Stock Options that have an exercise price of $10.13 per share expiring June 2, 2029, 4,135 Stock Options that have an exercise price of $62.50 per share expiring June 7, 2030, which will vest on the earlier of June 8, 2021 or one day prior to the next annual meeting of the Issuer’s stockholders, and 7,106 Stock Options that have an exercise price of $54.12 per share expiring June 29, 2030, which will vest on the earlier of June 30, 2021 or one day prior to the next annual meeting of the Issuer’s stockholders. The policy of the Adviser to the Funds does not permit managing members of the Adviser GP to receive compensation for serving as directors of the Issuer, and the Funds are instead entitled to the pecuniary interest in any compensation received for their service.

(c) Neither the Reporting Persons nor their affiliates has effected any other transactions in securities of the Issuer during the past 60 days.

(d) Certain securities of the Issuer are held directly by 667, a limited partnership the sole general partner of which is Baker Biotech Capital, L.P., a limited partnership the sole general partner of which is Baker Biotech Capital (GP), LLC. Julian C. Baker and Felix J. Baker are the managing members of Baker Biotech Capital (GP), LLC.

Certain securities of the Issuer are held directly by Life Sciences, a limited partnership the sole general partner of which is Baker Brothers Life Sciences Capital, L.P., a limited partnership the sole general partner of which is Baker Brothers Life Sciences Capital (GP), LLC. Julian C. Baker and Felix J. Baker are the managing members of Baker Brothers Life Sciences Capital (GP), LLC.

(e) Not applicable.

Item 6.

Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer.

Item 6 of this Schedule 13D is supplemented and superseded, as the case may be, as follows:

Registration Rights Agreement

On March 1, 2021, the Funds, along with D. Victor Perlroth, M.D., entered into a registration rights agreement (the “Registration Rights Agreement”) with the Issuer pursuant to which the Funds are entitled to certain resale registration rights with respect to shares of Common Stock of the Issuer issued or issuable upon the conversion of any securities of the Issuer that are now held or are hereafter acquired by the Funds (the “Registrable Securities”).

Under the Registration Rights Agreement, following a request by the Funds, the Issuer is obligated to file a resale registration statement on Form S-3, or other appropriate form, covering Registrable Securities held by the Funds (the “Resale Registration Shelf”), and to keep the Resale Registration Shelf effective until the earlier of such time that (i) all Registrable Securities covered by the Resale Registration Statement have been sold or may be sold freely without limitations or restrictions as to volume or manner of sale pursuant to Rule 144 of the Securities Act of 1933, as amended, or (ii) all Registrable Securities covered by the Resale Registration Statement otherwise cease to be considered Registrable Securities pursuant to the terms of the Registration Rights Agreement. Under the Registration Rights Agreement, the Funds have the right to one underwritten public offering per calendar year, but no more than three underwritten public offerings in total and no more than two underwritten offerings or block trades in any twelve-month period, to effect the sale or distribution of their Registrable Securities, subject to specified exceptions, conditions and limitations. The rights of the Funds under the Registration Rights Agreement will continue in effect for up to ten years.

The foregoing description of the Registration Rights Agreement does not purport to be complete and is qualified in its entirety by reference to the full text of the Registration Rights Agreement, which is incorporated by reference as Exhibit 99.1 and is incorporated herein by reference.

2022 Warrant Agreement

Pursuant to a Warrant to Purchase Stock issued on August 11, 2017 (the “2022 Warrant Agreement”), 667 and Life Sciences hold, respectively, 11,184 and 138,815 warrants to purchase Common Stock at an exercise price of $0.01 per share and with an expiration date of August 11, 2022.

The foregoing description of the 2022 Warrant Agreement does not purport to be complete and is qualified in its entirety by reference to the full text of the 2022 Warrant Agreement, the form of which is incorporated by reference as Exhibit 99.2 and is incorporated herein by reference.

Item 7.

Material to be Filed as Exhibits.

Exhibit	Description
99.1	Registration Rights Agreement, by and among Kodiak Sciences Inc., 667, L.P., and Baker Brothers Life Sciences, L.P., dated as of March 1, 2021 (incorporated by reference to Exhibit 4.7 to the Issuer’s Annual Report on Form 10-K, filed with the SEC on March 1, 2021).
99.2	Form of Warrant to Purchase Stock (incorporated by reference to Exhibit 4.5 to the Issuer’s Registration Statement on Form S-1, filed with the SEC on September 7, 2018).

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.

March 5, 2021

	BAKER BROS. ADVISORS LP By: Baker Bros. Advisors (GP) LLC, its general partner

	By:	/s/ Scott L. Lessing
		Name: Scott L. Lessing Title: President

	BAKER BROS. ADVISORS (GP) LLC

	By:	/s/ Scott L. Lessing
		Name: Scott L. Lessing Title: President

	/s/ Julian C. Baker
	Julian C. Baker

	/s/ Felix J. Baker
	Felix J. Baker

SEC Form SC 13D/A filed