13D Filing: Baker Bros. Advisors and Beigene, Ltd. (BGNE)

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.   )*

BeiGene, Ltd.

(Name of Issuer)

Ordinary Shares, par value $0.0001 per
share

(Title of Class of Securities)

07725L102**

(CUSIP number)

Alexandra A. Toohey

Chief Financial Officer

Baker Bros. Advisors LP

667 Madison Avenue, 21^st Floor

New York, NY 10065

(212) 339-5690

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

February 8, 2016

(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 10 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.

**This CUSIP applies to the American Depository Shares, each
representing thirteen Ordinary Shares

CUSIP No.    07725L102

Page   2   of   10   Pages

1.	NAMES OF REPORTING PERSONS Baker Bros. Advisors LP
2.	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) ¨ (b) ¨
3.	SEC USE ONLY
4.	SOURCE OF FUNDS* OO
5.	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) or 2(e) o
6.	CITIZENSHIP OR PLACE OF ORGANIZATION Delaware
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH		7.	SOLE VOTING POWER: 105,199,597 (1)
		8.	SHARED VOTING POWER: 0
		9.	SOLE DISPOSITIVE POWER: 105,199,597 (1)
		10.	SHARED DISPOSITIVE POWER: 0
11.	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON: 105,199,597 (1)
12.	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES* ¨
13.	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11) 24.6% (2)
14.	TYPE OF REPORTING PERSON* IA, PN

(1)

Includes 24,864,840 of the Ordinary Shares reported as beneficially owned that are beneficially owned through American Depositary Shares. Each American Depositary Share represents 13 Ordinary Shares of the Issuer.

(2)

Based on 427,442,865 Ordinary Shares outstanding as of February 8, 2016, according to information received from the Issuer on February 9, 2016.

CUSIP No.    07725L102

Page   3   of   10   Pages

1.	NAMES OF REPORTING PERSONS Baker Bros. Advisors (GP) LLC
2.	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) ¨ (b) ¨
3.	SEC USE ONLY
4.	SOURCE OF FUNDS* OO
5.	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) or 2(e) o
6.	CITIZENSHIP OR PLACE OF ORGANIZATION Delaware
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH		7.	SOLE VOTING POWER: 105,199,597 (1)
		8.	SHARED VOTING POWER: 0
		9.	SOLE DISPOSITIVE POWER: 105,199,597 (1)
		10.	SHARED DISPOSITIVE POWER: 0
11.	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON: 105,199,597 (1)
12.	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES* ¨
13.	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11) 24.6% (2)
14.	TYPE OF REPORTING PERSON* HC, OO

(1)

Includes 24,864,840 of the Ordinary Shares reported as beneficially owned that are beneficially owned through American Depositary Shares. Each American Depositary Share represents 13 Ordinary Shares of the Issuer.

(2)

Based on 427,442,865 Ordinary Shares outstanding as of February 8, 2016, according to information received from the Issuer on February 9, 2016.

CUSIP No.    07725L102

Page   4   of   10   Pages

1.	NAMES OF REPORTING PERSONS Felix J. Baker
2.	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) ¨ (b) ¨
3.	SEC USE ONLY
4.	SOURCE OF FUNDS* OO
5.	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) or 2(e) o
6.	CITIZENSHIP OR PLACE OF ORGANIZATION United States
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH		7.	SOLE VOTING POWER: 105,199,597 (1)
		8.	SHARED VOTING POWER:
		9.	SOLE DISPOSITIVE POWER: 105,199,597 (1)
		10.	SHARED DISPOSITIVE POWER:
11.	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON: 105,199,597 (1)
12.	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES* ¨
13.	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11) 24.6% (2)
14.	TYPE OF REPORTING PERSON* IN, HC

(1)

Includes 24,864,840 of the Ordinary Shares reported as beneficially owned that are beneficially owned through American Depositary Shares. Each American Depositary Share represents 13 Ordinary Shares of the Issuer.

(2)

Based on 427,442,865 Ordinary Shares outstanding as of February 8, 2016, according to information received from the Issuer on February 9, 2016.

CUSIP No.    07725L102

Page   5   of   10   Pages

1.	NAMES OF REPORTING PERSONS Julian C. Baker
2.	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) ¨ (b) ¨
3.	SEC USE ONLY
4.	SOURCE OF FUNDS* OO
5.	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) or 2(e) o
6.	CITIZENSHIP OR PLACE OF ORGANIZATION United States
NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH		7.	SOLE VOTING POWER: 105,199,597 (1)
		8.	SHARED VOTING POWER:
		9.	SOLE DISPOSITIVE POWER: 105,199,597 (1)
		10.	SHARED DISPOSITIVE POWER:
11.	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON: 105,199,597 (1)
12.	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES* ¨
13.	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11) 24.6% (2)
14.	TYPE OF REPORTING PERSON* IN, HC

(1)

Includes 24,864,840 of the Ordinary Shares reported as beneficially owned that are beneficially owned through American Depositary Shares. Each American Depositary Share represents 13 Ordinary Shares of the Issuer.

(2)

Based on 427,442,865 Ordinary Shares outstanding as of February 8, 2016, according to information received from the Issuer on February 9, 2016.

Schedule 13D

ITEM 1. Security and Issuer.

The
class of equity securities to which this statement on Schedule 13D relates is the Ordinary Shares, par value $0.0001per share (the “Ordinary Shares”) of BeiGene Ltd., a corporation
organized under the laws of the Cayman Islands (the “Issuer”). The address of the principal executive offices of the
Issuer is c/o Mourant Ozannes Corporate Services (Cayman) Limited, 94 Solaris Avenue, Camana Bay, Grand Cayman KY1-1108, Cayman
Islands. Information given in response to each item shall be deemed
incorporated by reference in all other items, as applicable.

 

ITEM 2. Identity and Background.

 

(a) The Reporting Persons are:

1.

Baker Bros. Advisors LP (the “Adviser”)

2.

Baker Bros. Advisors (GP) LLC (the “Adviser GP”)

3.

Felix J. Baker

4.

Julian C. Baker

(b) The business address of each of the Reporting Persons is:

c/o Baker Bros. Advisors LP

667 Madison Avenue, 21^st Floor

New York, NY 10065

(212) 339-5690

(c) The Adviser is an entity engaged in investment activities,
and the Adviser GP is in the business of acting as its general partner and, through the Adviser, investment activities. The principal
business of each of Julian C. Baker and Felix J. Baker is to serve as a managing member of the Adviser GP.

(d) and (e) During the past five years, none of the Reporting
Persons nor any of the Funds (as defined below) has been (i) convicted in a criminal proceeding (excluding traffic violations or
similar misdemeanors) or (ii) a party to a civil proceeding of a judicial or administrative body of competent jurisdiction and
as a result of such proceeding was or is subject to a judgment, decree or final order enjoining future violations of, or prohibiting
or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws.

(f) The Adviser GP is a limited liability company organized
under the laws of the State of Delaware. The Adviser is a limited partnership organized under the laws of the State of Delaware.
The citizenship of each of Julian C. Baker and Felix J. Baker is the United States of America.

 

Item 3. Source and Amount of Funds or Other Consideration

The disclosure in Item 4 below is incorporated herein by reference.

The securities of the Issuer reported herein were purchased
and acquired by 667, L.P. (“667”), Baker Brothers Life Sciences, L.P. (“Life Sciences”) and 14159, L.P.
(“14159” and together with 667 and Life Sciences, the “Funds”) with the working capital of the Funds both
in transactions with the underwriters (as described below) and as a result of conversions and exercise of securities formerly acquired
in private transactions directly with the Issuer. The aggregate purchase price of the securities of the Issuer directly held by
the Funds was approximately $114,091,819.

Item 4. Purpose of the Transaction.

On February 3, 2016, BeiGene, Ltd. (“the Issuer”)
entered into an underwriting agreement (the “Underwriting Agreement”) with Goldman, Sachs & Co, Morgan Stanley
& Co. LLC, Cowen and Company LLC and Robert W. Baird & Co. Incorporated (the “Underwriters”), related to an
initial public offering (the “IPO”) of 6,600,000 American Depository Shares (“ADS”) of the Issuer at a
price to the public of $24.00 per share. Each ADS represents 13 ordinary shares. In addition, the Issuer granted the Underwriters
an option exercisable for 30 days from the date of the Underwriting Agreement to purchase, at the public offering price less any
underwriting discounts and commissions, up to an additional 990,000 ADS to cover overallotments, if any. The IPO closed on February
8, 2016.

Pursuant to the IPO, on February 8, 2016, 667 and Life Sciences
purchased 189,374 and 1,723,306 ADS, respectively, at the offering price of $24.00 per share, totaling 1,912,680 ADS in the aggregate.
Each of 667 and Life Sciences purchased the ADS with their working capital.

On February 8, 2016, upon the closing of the IPO, 667, Life
Sciences and 14159 acquired 4,382,118, 44,572,171 and 582,747 Ordinary Shares, respectively, resulting from the conversion of Series
A Preferred Shares of the Issuer (“Preferred Series A”). Additionally, Life Sciences and 667 acquired 1,912,167 and
26,292,961 Ordinary Shares, respectively, resulting from the conversion of Series A-2 Preferred Shares of the Issuer (“Preferred
Series A-2”) The Preferred Series A and Preferred Series A-2 converted automatically upon the closing of the IPO for no consideration
on a 1 for 1 basis.

On February 8, 2016, the Funds exercised their warrants to purchase
Ordinary shares of the Issuer (“Warrants”) at an exercise price of $0.675 per ordinary share. 667, Life Sciences, and
14159 exercised 238,850, 2,296,890 and 56,853 Warrants, respectively, for an exercise price of $0.675 per Warrant using their working
capital.

Michael Goller and Ranjeev Krishana, employees of the Adviser,
have served on the Board of Directors of the Issuer (the “Board”) since April 21, 2015 and October 7, 2014, respectively.
Prior to serving on the Board, Michael Goller was a Board observer. Michael Goller and Ranjeev Krishana currently serve on the
Board as representatives of the Funds. The policy of the Funds and the Adviser does not permit principals or employees of the Adviser
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.

The Funds hold securities of the Issuer for investment purposes.
The Reporting Persons or their affiliates may purchase additional securities or dispose of securities in varying amounts and at
varying times depending upon the Reporting Persons’ continuing assessments of pertinent factors, including the availability
of shares of common stock or other securities for purchase at particular price levels, the business prospects of the Issuer, other
business investment opportunities, economic conditions, stock market conditions, money market conditions, the attitudes and actions
of the Board and management of the Issuer, the availability and nature of opportunities to dispose of securities of the Issuer
and other plans and requirements of the particular entities. The Reporting Persons may discuss items of mutual interest with the
Issuer, which could include items in subparagraphs (a) through (j) of Schedule 13D.

Depending upon their assessments of the above factors, the Reporting
Persons or their affiliates may change their present intentions as stated above and they may assess whether to make suggestions
to the management of the Issuer regarding financing, and whether to acquire additional securities of the Issuer (by means of open
market purchases, privately negotiated purchases, or otherwise) or to dispose of some or all of the securities of the Issuer under
their control.

Except as otherwise disclosed herein, at the present time, the
Reporting Persons do not have any plans or proposals with respect to any extraordinary corporate transaction involving the Issuer
including, without limitation, those matters described in subparagraphs (a) through (j) of Item 4 of Schedule 13D.

 

 

ITEM 5. Interest in Securities of the Issuer.

(a) and (b) Items 7 through 11 and 13 of each of the cover pages
of this Schedule 13D are incorporated herein by reference.

The information set forth in Item 4 is hereby incorporated by
reference into this Item 5.

 

Set
forth below is the aggregate number of Ordinary Shares of Common Stock of the Issuer directly held and owned through ADS directly
held by the Funds and the percentage of the Issuer’s outstanding Ordinary Shares such holdings represent. Each ADS
represents 13 Ordinary Shares of the Issuer. The information set forth below is based upon 427,442,865 Ordinary Shares outstanding
as of February 8, 2016, according to information obtained from the Issuer on February 9, 2016. Such percentage figures are calculated
in accordance with Rule 13d-3 under the Securities Exchange Act of 1934, as amended.

Name		Number of Ordinary Shares we own or have the right to acquire within 60 days				Percent of Class Outstanding
667, L.P.			8,994,997				2.1	%
Baker Brother Life Sciences, L.P.			95,565,000				22.4	%
14159, L.P.			639,600				0.1	%
Total			105,199,597				24.6	%

Pursuant to management agreements, as amended, 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 Schedule 13D 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, except to the extent that any such Reporting
Persons actually exercises voting or dispositive power with respect to such securities.

(c) The information set forth in Item 4 is
hereby incorporated by reference into this Item 5(c). Except as disclosed herein, none of the Reporting Persons or 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 controlling 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 controlling
members of Baker Brothers Life Sciences Capital (GP), LLC.

Certain securities of the Issuer are held directly by 14159,
a limited partnership the sole general partner of which is 14159 Capital, L.P., a limited partnership the sole general partner
of which is 14159 Capital (GP), LLC. Julian C. Baker and Felix J. Baker are the controlling members of 14159 Capital (GP), LLC.

(e) Not applicable.

ITEM 6. Contracts,
Arrangements, Understandings or Relationships With Respect to Securities of the Issuer.

 

The information in Item 4 is incorporated by reference herein.

Item 7. Material to be Filed as Exhibits.

Exhibit	Description
99.1	Agreement Regarding the Joint Filing of Schedule 13D by and among the Reporting Persons.

 

 

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 9, 2016

	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