Exhibit 10.1

CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT HAS BEEN OMITTED
BECAUSE IT IS BOTH (I) NOT MATERIAL AND (II) WOULD LIKELY CAUSE COMPETITIVE HARM
TO ZYMEWORKS INC. IF PUBLICLY DISCLOSED. INFORMATION THAT HAS BEEN OMITTED HAS
BEEN NOTED IN THIS DOCUMENT WITH A PLACEHOLDER IDENTIFIED BY THE MARK “[…***…]”.

CONFIDENTIAL
FIRST AMENDMENT TO
COLLABORATION AGREEMENT

This First Amendment (the “Amendment”) to the Agreement (as defined below), is
entered into as of May 25, 2020 (the “Amendment Effective Date”), by and between
Zymeworks Inc., a corporation organized and existing under the laws of British
Columbia (“Zymeworks”), having a place of business at 540-1385 West 8th Avenue,
Vancouver, BC, Canada V6H 3V9, and BeiGene, Ltd., a Cayman Island exempted
company incorporated with limited liability (“BeiGene”), having a place of
business at c/o Mourant Ozannes Corporate Services (Cayman) Limited, 94 Solaris
Avenue, Camana Bay, PO Box 1348, Grand Cayman KY1-1108, Cayman Islands.
Zymeworks and BeiGene are each referred to individually as a “Party” and
together as the “Parties”.

BACKGROUND
A.Zymeworks and BeiGene entered into that certain License and Collaboration
Agreement dated November 26, 2018 pursuant to which BeiGene obtained an
exclusive license under certain patents and know-how controlled by Zymeworks to
develop and commercialize Zymeworks’ proprietary bispecific HER2 antibody-drug
conjugate known as ZW49 in the Field in the Territory (the “Agreement”).
B.Zymeworks is conducting clinical development of the Licensed Product outside
the Territory and wishes to expand the scope of its clinical development of
Licensed Product to certain countries in the Territory (as further described
below).
C.BeiGene wishes for Zymeworks to conduct such clinical development in such
countries in the Territory.
D.The Parties now desire to amend the Agreement as set forth herein.
        NOW THEREFORE, in consideration of the mutual covenants and agreements
contained herein below, the sufficiency of which is acknowledged by both
Parties, the Parties agree as follows as of the Amendment Effective Date:
AGREEMENT
1.Definitions. Unless otherwise defined in this Amendment, initially capitalized
terms used herein shall have the meanings given to them in the Agreement.
2.Article 1. Definitions. Article 1 of the Agreement is hereby amended as
follows:
a.Section 1.18 of the Agreement is hereby deleted in its entirety and replaced
with the following:

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“1.18 “Completion” means, (a) with respect to Dose Escalation Studies, the date
on which […***…] and (b) with respect to the Phase 1 Clinical Trial, the date on
which […***…].1”
b.The following definitions are hereby added as Sections 1.70 and 1.71,
respectively, of the Agreement, and the current Section 1.70 (Additional
Definitions) of the Agreement is hereby renumbered as Section 1.72:

“1.70 “Dose Escalation Studies” means a Phase 1 Clinical Trial, or portion
thereof, in which subjects are dosed with increasing doses of Licensed Product
to establish (a) the maximum tolerated dose of such Licensed Product and (b) one
or more recommended doses of such Licensed Product for use in further clinical
development of Licensed Product.”

“1.71 “Zymeworks Territory Studies” means any and all Clinical Trials set forth
in the Global Development Plan, other than the ZW49 Multi-Regional
Registrational Studies, to the extent such Clinical Trials are to be conducted
by Zymeworks in South Korea, New Zealand, Australia or […***…].2”
3.Section 4.1 Technology Transfer. Section 4.1 of the Agreement is hereby
deleted in its entirety and replaced with the following:

“4.1 Technology Transfer. The Parties acknowledge that as of the Amendment
Effective Date, Zymeworks has transferred to BeiGene certain Zymeworks Know-How
existing as of the Effective Date (the “Initial Technology Transfer”). Upon
Completion of the Phase 1 Clinical Trial for the Licensed Product, Zymeworks
shall promptly notify BeiGene in writing, including a copy of the results and
other existing information relevant thereto (the “Clinical Trial Results”)
(collectively, the “Trial Completion Notice”). Upon Completion of the Dose
Escalation Study Zymeworks will promptly notify BeiGene in writing of Completion
of the Dose Escalation Study, including a copy of the results and the
recommended dose for the Licensed Product (collectively, the “Dose
Identification Notice”). Within […***…] of the earlier of BeiGene’s receipt of
(a) the Trial Completion Notice or (b) Dose Identification Notice, Zymeworks
will provide and transfer to BeiGene, […***…], the Zymeworks Know-How that
exists as of the date of such Trial Completion Notice or Dose Identification
Notice and was not previously provided to BeiGene by providing copies or samples
of relevant documentation, materials and other embodiments of such Zymeworks
Know-How, including data within reports, and electronic files, that exists on
the Effective Date (the “Secondary Technology Transfer”). During the Term,
Zymeworks shall (i) at each meeting of the JSC (and, in any event, on […***…] if
any JSC meeting is not held in a particular […***…]), provide BeiGene with a
summary of additional Zymeworks Know-How, if any, developed since the last
meeting of the JSC, (ii) transfer any such Zymeworks Know-How to BeiGene
promptly following BeiGene’s reasonable request, (iii) transfer a copy of the
results of the Zymeworks Territory Studies to BeiGene, promptly after completion
of each such study; and (iv) provide BeiGene with reasonable access to Zymeworks
personnel involved in the research and Development of Licensed Products, either
in-person at Zymeworks’ facility or by teleconference (the “Continuing
Technology Transfer,” and together with the Initial Technology Transfer and the
Secondary Technology Transfer, the “Technology Transfer”). For the avoidance of
doubt, Zymeworks’ personnel shall not be obligated to travel to BeiGene’s
facilities, and Zymeworks’ transfer obligations under this Section 4.1 shall
apply solely to the extent the Zymeworks Know-How is reasonably necessary to
support BeiGene’s Development and

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Commercialization of the Licensed Product in the Field in the Territory in
accordance with this Agreement. Notwithstanding the foregoing, Zymeworks’
technology transfer obligations hereunder shall not include the obligation to
transfer manufacturing-related Know-How, except as set forth in Section 7.2 or
unless otherwise mutually agreed by the Parties in writing. 3”
4.Section 5.1 Diligence and Responsibilities. Section 5.1 of the Agreement is
hereby deleted in its entirety and replaced with the following:

        “5.1 Diligence and Responsibilities. […***…], BeiGene shall be
responsible for the Development of the Licensed Products in the Field in the
Territory in accordance with this Article 5. […***…], BeiGene shall use
Commercially Reasonable Efforts to (i) […***…], and (ii) […***…]. BeiGene shall
conduct such tasks in a timely, professional manner and in compliance with the
Territory Development Plan and Global Development Plan, as applicable, and all
Applicable Laws, including GLP, GCP and cGMP. […***…].4”
5.Section 5.2 Global Development Plan. Section 5.2 of the Agreement is hereby
amended as follows:
a.The first sentence of Section 5.2(b) of the Agreement is hereby deleted in its
entirety and replaced with the following:

“[…***…], BeiGene shall use Commercially Reasonable Efforts to perform the
Development activities assigned to BeiGene under the Global Development Plan to
support the global Development and registration of Licensed Products, […***…].5”
b.The following new Section 5.2(c) is hereby appended to Section 5.2 of the
Agreement to the end thereof:

         “(c) Notwithstanding anything to the contrary herein (including
Sections 5.1, 5.2(b) and 6.1), (i) Zymeworks will have the sole right, and shall
use Commercially Reasonable Efforts, […***…]; (ii) […***…]; and (iii) Zymeworks,
or its designee, will hold all Regulatory Submissions for the Zymeworks
Territory Studies, and will control all correspondence and interactions with
Regulatory Authorities with respect thereto, unless and until such Regulatory
Submissions are assigned to BeiGene pursuant to Section 6.1.6”
6.Section 5.7 Development Reports. Section 5.7 of the Agreement is hereby
amended to append the following new Section 5.7(b) to the end thereof and the
current language in Section 5.7 of the Agreement is hereby renumbered as Section
5.7(a):

“(b) Zymeworks shall provide BeiGene with […***…] written reports, […***…],
summarizing its conduct of (and Manufacture of Licensed Product for) the
Zymeworks Territory Studies, including a summary of the results of such
Zymeworks Territory Studies, which reports shall be in English. Subject to
BeiGene’s right to use and disclose data and results in accordance with Section
5.8 and the licenses and rights to Zymeworks IP granted to BeiGene in Section
2.1, such reports shall be

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Confidential Information of Zymeworks pursuant to Article 10. The Parties shall
discuss the status, progress and results of Zymeworks Territory Studies at JSC
meetings. 7”
7.Section 5.8 Data Exchange and Use. The first sentence of Section 5.8 of the
Agreement is hereby deleted in its entirety and replaced with the following:

“In addition to its adverse event and safety data reporting obligations pursuant
to Section 6.4, each Party shall promptly (but in any event no later than
[…***…] from the other Party’s request) provide the other Party with copies of
all data and results, including all Clinical Data, and all supporting
documentation (e.g. protocols, CRFs, analysis plans) Controlled by such Party or
its Affiliates that are generated by or on behalf of such Party or its
Affiliates or sublicensees, if applicable, in the Development of Licensed
Products, including, with respect to Zymeworks, in the conduct of the Zymeworks
Territory Studies; provided that Zymeworks shall only be required to provide
BeiGene such data, results and documentation to the extent it comprises
Zymeworks Know-How and is reasonably necessary or useful for BeiGene’s
Development or Commercialization of the Licensed Products in the Field in the
Territory, including any such data, results and documentation that are
reasonably requested by BeiGene or that are necessary to support filings for
Regulatory Approval for the Licensed Product in the Territory. 8”
8.Section 6.1 Holder of Regulatory Approvals and Regulatory Submissions. Section
6.1 of the Agreement is hereby deleted in its entirety and replaced with the
following:

“6.1 Holder of Regulatory Approvals and Regulatory Submissions. BeiGene shall be
the holder of Regulatory Approvals and Regulatory Submission for Licensed
Products in the Field in the Territory, except as expressly set forth in Section
5.2(c) with respect to the Zymeworks Territory Studies. Zymeworks shall
reasonably cooperate with BeiGene, at BeiGene’s request and expense, to enable
BeiGene to obtain any or all such Regulatory Approvals and Regulatory
Submissions. Such cooperation may include transferring the Regulatory
Submissions for the Zymeworks Territory Studies to BeiGene, if necessary to
enable BeiGene to fulfill its obligations to enroll patients in South Korea,
Australia, New Zealand and […***…] in the ZW49 Multi-Regional Registrational
Studies in accordance with the Global Development Plan. 9”
9.Section 6.4 Adverse Event Reporting. Section 6.4 of the Agreement is hereby
deleted in its entirety and replaced with the following:

“6.4 Adverse Events Reporting. Promptly following BeiGene’s receipt of (x) the
Trial Completion Notice or (y) the Dose Identification Notice, whichever occurs
first, but in no event later than […***…] thereafter, BeiGene and Zymeworks
shall develop and agree in a written agreement to worldwide safety and
pharmacovigilance procedures for the Parties with respect to Licensed Products,
such as safety data sharing and exchange, adverse events reporting and
prescription events monitoring (the “Pharmacovigilance Agreement”). Such
Pharmacovigilance Agreement shall (a) describe the obligations of both Parties
with respect to the coordination of collection, investigation, reporting and
exchange of information between the Parties concerning adverse events or any
other safety issue of any significance and product quality and product
complaints involving adverse events, in each case with respect to Licensed
Products and sufficient to permit each Party and its Affiliates, licensees or

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sublicensees to comply with its legal obligations with respect thereto; (b) be
promptly updated if required by changes in Applicable Law; (c) provide that (i)
BeiGene shall maintain an adverse event database for Clinical Trials conducted
in the Territory under the Territory Development Plan and the Global Development
Plan, […***…]; (ii) BeiGene shall be responsible for (A) reporting to the
applicable Regulatory Authorities in the Territory, all quality complaints,
adverse events and safety data related to Licensed Products for all Clinical
Trials conducted in the Territory under the Territory Development Plan or the
Global Development Plan, (B) responding, to safety issues and to all requests of
Regulatory Authorities related to such safety issues with respect to the
Licensed Products in the Field in the Territory, in each case ((i) and (ii)),
other than the Zymeworks Territory Studies, with respect to which Zymeworks will
retain such responsibilities and will keep BeiGene reasonably informed until
such time as the Regulatory Submissions for the Zymeworks Territory Studies are
assigned to BeiGene pursuant to Section 6.1, at which time BeiGene will assume
such responsibilities; (iii) BeiGene shall provide to Zymeworks access to
BeiGene’s adverse event database for the Licensed Product in the Territory; (iv)
Zymeworks shall maintain a global adverse event database for the Licensed
Products, including with respect to Clinical Trials conducted under the Global
Development Plan, at Zymeworks’ cost and expense, except for any costs allocated
to BeiGene pursuant to Section 5.4; and (v) Zymeworks will provide BeiGene with
adverse event information regarding the Licensed Products in accordance with the
PV Agreement; and (d) include the following definition of “adverse event”: any
untoward medical occurrence in a patient or clinical investigation subject
administered a pharmaceutical product and which does not necessarily have a
causal relationship with this treatment; an adverse event can therefore be any
unfavorable and unintended sign (including an abnormal laboratory finding),
symptom, or disease temporally associated with the use of a medicinal product,
whether or not related to the medicinal product.10”
10.Section 7.2. The first sentence of Section 7.2 of the Agreement is hereby
deleted in its entirety and replaced with the following:

“7.2 Manufacturing Technology Transfer. In addition to the Zymeworks Know-How
provided to BeiGene pursuant to the Initial Technology Transfer and any
Secondary Technology Transfer, upon BeiGene’s written request, after the earlier
of: (a) […***…], and (b) […***…], Zymeworks will promptly prepare and submit to
the JSC, for its review, a plan (“Manufacturing Technology Transfer Plan”) for
the transfer to BeiGene of all Know-How Controlled by Zymeworks with respect to
the Manufacture of Licensed Product (“Zymeworks Manufacturing IP”), and the
conduct by Zymeworks of such consultation activities, as are necessary to enable
BeiGene or any Third Party contract manufacturing organization (the “CMO”)
designated by BeiGene and agreed by the Parties in writing to manufacture for
the Territory (a) the Licensed Antibody-Drug Conjugate as the Active Ingredient
of the applicable Licensed Product and/or (b) the applicable Licensed Product
(such actions, “Manufacturing Technology Transfer”).11”
11.Section 7.3(a) Supply by Zymeworks. The first paragraph of Section 7.3(a) of
the Agreement (but not, for clarity, Sections 7.3(a)(i) and 7.3(a)(ii) of the
Agreement) is hereby deleted in its entirety and replaced with the following:

“(a)  Development Supply. Subject to Sections 7.2 and 7.3(b), Zymeworks shall
have the right, either by itself or through a Third Party contract manufacturer,
to manufacture and supply to

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BeiGene all Licensed Products required by BeiGene for Development use in the
Territory under the Territory Development Plan and for BeiGene’s
Development-related responsibilities under the Global Development Plan,
including the conduct of any ZW49 Multi-Regional Clinical Study. Subject to
Section 7.2, the Parties shall use Commercially Reasonable Efforts to enter into
an agreement governing the supply by Zymeworks of such Licensed Products for
such Development use by BeiGene (“Clinical Supply Agreement”) within […***…]
following BeiGene's receipt of (x) the Trial Completion Notice or (y) the Dose
Identification Notice, whichever occurs first, pursuant to which:12”
12.Section 9.2 Development Milestones. Section 9.2 of the Agreement is hereby
amended to append the following to the end thereof after the table setting forth
Development Milestones Events:

“For clarity, any activities conducted by or on behalf of Zymeworks with respect
to the […***…] will not trigger a Development Milestone Event. For further
clarity, neither BeiGene nor its Affiliates shall be deemed to be acting “on
behalf of” Zymeworks for purposes of the foregoing sentence.13”
13.Section 11.1(c) Publications. The second sentence of Section 11.1(c) of the
Agreement is hereby deleted in its entirety and replaced with the following:

“In the event Zymeworks desires to publicly present or publish a Zymeworks
Publication that includes data from a Clinical Trial site in the Territory in
accordance with the foregoing sentence, including any Zymeworks Publication with
respect to Clinical Trial Results or Clinical Data generated in conduct of the
Zymeworks Territory Studies, Zymeworks shall provide BeiGene (including the
Alliance Manager and all BeiGene members of the JSC) with a copy of such
proposed Zymeworks Publication consistent with the applicable Review Period.”
14.Sections 12.5(b) and 12.5(c) Covenants of Zymeworks. Sections 12.5(b) and
12.5(c) of the Agreement are hereby deleted in its entirety and replaced with
the following:

“(b)  Zymeworks will conduct its obligations with respect to the Zymeworks
Territory Studies and the ZW49 Multi-Regional Registrational Study under the
Global Development Plan in strict adherence with the study design set forth in
the protocol for such Zymeworks Territory Study or ZW49 Multi-Regional
Registrational Study, as applicable, and as set forth in the Global Development
Plan, each as may be amended from time to time, and will comply with the
statistical analysis plan implemented by Zymeworks in connection therewith;

(c) Zymeworks will only engage Clinical Trial sites under the Global Development
Plan, including for the Zymeworks Territory Studies, that conduct all Clinical
Trials in compliance with Applicable Laws, including GCP and the ICH Guidelines,
and are approved by the applicable Regulatory Authority;”
15.Exhibit 5.2 ZW Global Development Plan. Exhibit 5.2 of the Agreement is
hereby deleted in its entirety and replaced with Exhibit 5.2 attached to this
Amendment.
16.No Other Modifications. Except as specifically set forth in this Amendment,
the terms and conditions of the Amendment shall remain in full force and effect.
No waiver of any obligation under this Amendment shall be effective unless it
has been given in writing and signed by the Party giving such waiver. No

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provision of this Amendment may be amended or modified other than by a written
document signed by authorized representatives of each Party.
17.Miscellaneous. This Amendment, together with the Agreement, sets forth the
entire agreement and understanding of the Parties as to the subject matter
hereof and supersedes all proposals, oral or written, and all other
communications between the Parties with respect to such subject matter. This
Amendment may be executed in two (2) or more counterparts, each of which shall
be deemed an original, but all of which together shall constitute one and the
same instrument. This Amendment shall be governed by and construed in accordance
with the laws of the State of New York and the patent laws of the United States
without reference to any rules of conflict of laws.

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IN WITNESS WHEREOF, the Parties intending to be bound have caused this Agreement
to be executed by their duly authorized representatives.

ZYMEWORKS INC.

By: /s/ Ali Tehrani 
Name: Ali Tehrani, Ph.D.
Title: President & Chief Executive Officer

BEIGENE, LTD.

By: /s/ Guillaume Vignon  
Name: Guillaume Vignon   
Title: SVP, Business Development  

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Exhibit 5.2
ZW49
GLOBAL DEVELOPMENT PLAN

[…***… ]14

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