UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No.      )*

Molecular Templates, Inc.

(Name of Issuer)

Common Stock, $0.001 par value

(Title of Class of Securities)

608550 109

(CUSIP Number)

James Kehoe

Takeda Pharmaceutical Company Limited

12-10, Nihonbashi 2-Chome, Chuo-ku, Tokyo 103-8668

Tel: +81 3 3278-2111

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

August 1, 2017

(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 which 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:  ☐

Note: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See Rule 13d-7 for other parties to whom copies are to be sent.

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 (“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).

SCHEDULE 13D

SCHEDULE 13D

CUSIP No. 608550  109

SCHEDULE 13D

CUSIP No. 608550  109

SCHEDULE 13D

CUSIP No. 608550  109

SCHEDULE 13D

CUSIP No. 608550  109

SCHEDULE 13D

CUSIP No. 608550  109

SCHEDULE 13D

CUSIP No. 608550  109

SCHEDULE 13D

Molecular Templates, Inc.

This Schedule 13D (the “Schedule 13D”) relates to the common stock, par value $0.001 per share (the “Common Stock”), of Molecular Templates, Inc., a Delaware corporation (the “Issuer”). The principal executive offices of the Issuer are located at 9301 Amberglen Blvd, Suite 100, Austin, Texas 78729.

On March 16, 2017, the Issuer (formerly known as “Threshold Pharmaceuticals, Inc.”) and Molecular Templates, Inc., a private company (“MTEM”), entered into an Agreement and Plan of Merger and Reorganization (the “Merger Agreement”). Pursuant to the terms of the Merger Agreement, on July 31, 2017, a wholly-owned subsidiary of the Issuer merged with and into MTEM, with MTEM surviving the Merger as a wholly-owned subsidiary of the Issuer (the “Merger”). At the effective time of the Merger, each outstanding share of MTEM’s common stock (subject to certain exceptions) converted into 7.7844 shares of the Issuer’s common stock. Following completion of the Merger, the Issuer was renamed “Molecular Templates, Inc.”

Following the closing of the Merger, on August 1, 2017, the Issuer closed a private placement pursuant to which certain investors purchased 5,793,063 equity units, each comprised of one share of Common Stock and a warrant to purchase 0.50 shares of Common Stock, at a purchase price of $6.9048 per unit (the “Concurrent Financing”).

Following the closing of the Concurrent Financing, on August 1, 2017, the Issuer closed a private placement with Millennium Pharmaceuticals, Inc., pursuant to which it sold to Millennium Pharmaceuticals, Inc. 2,922,993 shares of Common Stock at a purchase price of $6.8423 per share (the “Takeda Financing”). The Concurrent Financing and the Takeda Financing are referred to collectively in this Schedule 13D as the “Private Placements.”

This Schedule 13D is being jointly filed on behalf of: (i) Takeda Pharmaceutical Company Limited, a corporation organized under the laws of Japan (“Takeda”); (ii) Millennium Pharmaceuticals, Inc., a Delaware corporation (“Millennium”); (iii) Takeda Pharmaceuticals U.S.A., Inc., a Delaware Corporation (“Takeda USA”); (iv) Takeda Pharmaceuticals International AG, a Swiss joint stock corporation (“Takeda International”); (v) Takeda Pharma A/S, a Danish stock limited company (“Takeda Denmark”); (vi) Takeda A/S, a Danish stock limited company (“Takeda A/S”); and (vii) Takeda Europe Holdings B.V., a Dutch private limited company (“Takeda Europe”) (each of Takeda, Millennium, Takeda USA, Takeda International, Takeda Denmark, Takeda A/S and Takeda Europe, a “Reporting Person” and collectively, the “Reporting Persons”).

Takeda is the indirect parent company of Millennium. Millennium is a wholly-owned direct subsidiary of Takeda USA. Takeda owns 73.37% of Takeda USA, and Takeda International owns 26.63% of Takeda USA. Takeda Denmark owns 86.83% of Takeda International, and Takeda Europe owns 13.17% of Takeda International. Takeda Denmark is a wholly-owned direct subsidiary of Takeda A/S. Takeda owns 76.09% of Takeda A/S, and Takeda Europe owns 23.91% of Takeda A/S. Takeda Europe is a wholly-owned direct subsidiary of Takeda. Because of the relationship of Millennium to each of Takeda USA, Takeda International, Takeda Denmark, Takeda A/S, Takeda Europe and Takeda, each Reporting Person may be deemed to beneficially own the shares of Common Stock described herein. A Joint Filing Agreement among the Reporting Persons is attached as Exhibit 6 to this Schedule 13D.

The principal business address of Takeda is 12-10, Nihonbashi 2-chome, Chuo-ku, Tokyo 103-8668. The principal address of Millennium is 40 Landsdowne Street, Cambridge, Massachusetts, 02139. The principal address of Takeda USA is One Takeda Parkway, Deerfield, Illinois 60015. The principal address of Takeda International is Thurgauerstrasse 130, 8152 Glattpark, Switzerland. The principal address of Takeda Denmark is Langebjerg 1, 4000 Roskilde, Denmark. The principal address of Takeda A/S is Dybendal Alle 10, 2630 Taastrup, Denmark. The principal address of Takeda Europe is Jupiterstraat 250, 2132 HK Hoofddorp, Netherlands.

Takeda’s principal business is operating as a global, research and development-driven pharmaceutical company committed to bringing better health and a brighter future to patients by translating science into life-changing medicines, focusing its R&D efforts on oncology, gastroenterology and central nervous system therapeutic areas plus vaccines. Millennium is principally engaged in the business of conducting research, development and commercial functions of Takeda. Takeda USA is principally engaged in the business of serving as the U.S. commercial organization of Takeda. Takeda International is principally engaged in the business of conducting commercial and financial functions of Takeda. Takeda Denmark is principally engaged in the business of conducting marketing, manufacturing and development functions of Takeda. Each of Takeda Europe and Takeda A/S is principally engaged in the business of being an intermediate holding company of Takeda.

The name, business address, present principal occupation or employment and citizenship of each director and executive officer of each Reporting Person is set forth on Schedule I hereto.

During the last five years, none of the Reporting Persons or, to the knowledge of each of the Reporting Persons, any of the persons listed on Schedule I attached hereto has (i) been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors) or (ii) been 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.

The information set forth or incorporated in Items 4 and 6 hereof are incorporated herein by reference.

Millennium purchased the shares of Common Stock of the Issuer with working capital of Millennium set aside for the general purpose of investing.

The information set forth or incorporated in Items 3 and 6 hereof are incorporated herein by reference.

On October 31, 2016, Millennium entered into a Collaboration and Option Agreement with MTEM (the “First Collaboration Agreement”), which is attached as Exhibit 1 to this Schedule 13D. The purpose of the First Collaboration Agreement is to discover and develop engineered toxin bodies targeting CD38. Under the terms of the First Collaboration Agreement, MTEM is responsible for providing to Millennium (i) new engineered toxin bodies generated using Millennium’s proprietary fully human antibodies targeting CD38 and (ii) MTEM’s proprietary compound, MT-4019, for in vitro and in vivo pharmacological and anti-tumor efficacy evaluations. MTEM granted Millennium an exclusive option to negotiate and obtain an exclusive worldwide license to develop and commercialize any engineered toxin body that may result from this collaboration, including MT-4019.

On June 23, 2017, Millennium entered into a Multi-Target Collaboration and License Agreement with MTEM (the “Second Collaboration Agreement” and, together with the First Collaboration Agreement, the “Collaboration Agreements”), which is attached as Exhibit 2 to this Schedule 13D. Pursuant to the Second Collaboration Agreement, the parties will collaborate to identify, generate and evaluate engineered toxin bodies against certain targets designated by Millennium. Millennium will designate certain targets of interest as the focus of the research. Millennium will provide to MTEM targeting moieties against the designated targets. MTEM will create and characterize engineered toxin bodies against those targets and provide them to Millennium for further evaluation. Each party granted to the other nonexclusive rights in its intellectual property for purposes of the conduct of the research, and MTEM agreed to work exclusively with Millennium with respect to the designated targets. Under the agreement, Millennium has an option to acquire an exclusive license under MTEM’s intellectual property to develop, manufacture, commercialize and otherwise exploit engineered toxin bodies against the designated targets.

Concurrently with the Second Collaboration Agreement, Millennium entered into a Stock Purchase Agreement with MTEM and the Issuer (the “Stock Purchase Agreement”), which is attached as Exhibit 3 to this Schedule 13D. Pursuant to the Stock Purchase Agreement, Millennium agreed to purchase approximately $20.0 million of shares of Common Stock of the Issuer in a private placement, provided that Millennium’s investment amount would be

reduced to the extent its beneficial ownership post-closing would exceed 19.0% of the total outstanding shares of the Issuer. The transactions contemplated by the Stock Purchase Agreement (the Takeda Financing) were consummated on August 1, 2017, and Millennium purchased 2,922,993 shares of Common Stock for an aggregate purchase price of $19,999,995.00, or $6.8423 per share. Pursuant to the terms of the Stock Purchase Agreement, Millennium is restricted for a period of 180 days following the closing date of the Takeda Financing from certain sales or dispositions of the Issuer’s Common Stock.

In connection with the closing of the transactions contemplated by the Stock Purchase Agreement, the Issuer entered into a Restated Registration Rights Agreement (the “Registration Rights Agreement”) with Millennium and the investors in the Concurrent Financing, which is attached as Exhibit 4 to this Schedule 13D. Pursuant to the terms of the Registration Rights Agreement, the Issuer is obligated, among other things, to file a registration statement with the U.S. Securities and Exchange Commission within 45 days following the closing of the Concurrent Financing and Takeda Financing for purposes of registering the shares of Common Stock purchased in the Concurrent Financing and Takeda Financing and the shares issuable upon exercise of the warrants issued in the Concurrent Financing for resale by the investors, (ii) use its commercially reasonable efforts to have the registration statement declared effective as soon as practicable after filing, and in any event no later than 120 days after the closing of the Concurrent Financing and Takeda Financing and (iii) maintain the registration until all registrable securities may be sold pursuant to Rule 144 under the Securities Act of 1933, as amended, without restriction as to volume. The Registration Rights Agreement contains customary terms and conditions for a transaction of this type, including certain customary cash penalties on the Issuer for its failure to satisfy specified filing and effectiveness time periods.

Millennium acquired the shares of Common Stock reported on this Schedule 13D in furtherance of the purposes of the Collaboration Agreements.

Takeda intends to review its investment on a regular basis and, as a result thereof, may at any time or from time to time determine, either alone or as part of a group, (a) to acquire additional securities of the Issuer, through open market purchases, privately negotiated transactions or otherwise, (b) to dispose of all or a portion of the securities of the Issuer owned by it in the open market, in privately negotiated transactions or otherwise, or (c) to take any other available course of action, which could involve one or more of the types of transactions or have one or more of the results described in the next paragraph of this Item 4. Any such acquisition or disposition or other transaction would be made in compliance with all applicable laws and regulations. Notwithstanding anything contained herein, Takeda specifically reserves the right to change its intention with respect to any or all of such matters. In reaching any decision as to its course of action (as well as to the specific elements thereof), Takeda currently expects that it would take into consideration a variety of factors, including, but not limited to, the following: the Issuer’s business and prospects; other developments concerning the Issuer and its businesses generally; other business opportunities available to the Issuer; changes in law and government regulations; general economic conditions; and monetary and stock market conditions, including the market price of the securities of the Issuer.

Except as set forth above, Takeda does not have any present plans which relate to or would result in:

(a), (b) and (c) — The information contained on the cover pages to this Schedule 13D and the information set forth or incorporated in Items 2, 3, 4 and 6 hereof are incorporated herein by reference.

As of August 1, 2017, following the consummation of the Takeda Financing, Takeda beneficially owns 2,922,993 shares of Common Stock, representing approximately 10.9% of the shares of Common Stock outstanding as of such date, as determined based on 26,880,857 shares of Common Stock outstanding as of August 1, 2017.

(d) Not applicable.

(e) Not applicable.

The information set forth or incorporated in Item 4 hereof is incorporated herein by reference in response to this Item 6.

Michael Broxson, who is the Vice President and Head of R&D Business Development of Takeda, was appointed as a member of the board of directors of the Issuer on August 1, 2017. Mr. Broxson is a party to an indemnification agreement with the Issuer, pursuant to which the Issuer agrees to indemnify Mr. Broxson to the fullest extent permitted by law and public policy for claims arising in his capacity as a director of the Issuer. Mr. Broxson is only entitled to indemnification to the extent he acted in good faith and in a manner he reasonably believed to be in, or not opposed to, the best interests of the Issuer, and, with respect to any criminal proceeding, he had no reasonable basis to believe that his conduct was unlawful. Subject to the applicable provisions of the Delaware General Corporation Law, the Issuer will reimburse Mr. Broxson for expenses covered by the indemnification agreement within thirty days of Mr. Broxson’s request for such payment. A form of the indemnification agreement is attached as Exhibit 5 to this Schedule 13D.

Other than as described in Items 3, 4 and 5, this Item 6, and the agreements set forth as exhibits hereto, to the Reporting Person’s knowledge, there are no contracts, arrangements, understandings or relationships (legal or otherwise) among the persons named in Item 2 and between such persons and any person with respect to any securities of the Issuer.

SIGNATURE

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

EXHIBIT INDEX

SCHEDULE A

DIRECTORS AND EXECUTIVE OFFICERS OF THE REPORTING PERSONS

Takeda Pharmaceutical Company Limited

The name, business address, title and present principal occupation or employment of each of the directors and executive officers of Takeda Pharmaceutical Company Limited (“Takeda”) are set forth below. If no address is given, the business address is 12-10, Nihonbashi 2-chome, Chuo-ku, Tokyo 103-8668.

Millennium Pharmaceuticals, Inc.

The name, business address, title and present principal occupation or employment of each of the directors and executive officers of Millennium Pharmaceuticals, Inc. (“Millennium”) are set forth below. If no address is given, the business address is 40 Landsdowne Street, Cambridge, Massachusetts, 02139.

Takeda Pharmaceuticals USA, Inc.

The name, business address, title and present principal occupation or employment of each of the directors and executive officers of Takeda Pharmaceuticals U.S.A., Inc. (“Takeda USA”) are set forth below. If no address is given, the business address is One Takeda Parkway, Deerfield, Illinois 60015.

Takeda Pharmaceuticals International AG

The name, business address, title and present principal occupation or employment of each of the directors and executive officers of Takeda Pharmaceuticals International AG (“Takeda International”) are set forth below. If no address is given, the business address is Thurgauerstrasse 130, 8152 Glattpark, Switzerland.

Takeda Pharma A/S

The name, business address, title and present principal occupation or employment of each of the directors and executive officers of Takeda Pharma A/S (“Takeda Denmark”) are set forth below. If no address is given, the business address is Langebjerg 1, 4000 Roskilde, Denmark.

Takeda A/S

The name, business address, title and present principal occupation or employment of each of the directors and executive officers of Takeda A/S (“Takeda A/S”) are set forth below. If no address is given, the business address is Dybendal Alle 10, 2630 Taastrup, Denmark.

Takeda Europe Holdings B.V.

The name, business address, title and present principal occupation or employment of each of the directors and executive officers of Takeda Europe Holdings B.V. (“Takeda Europe”) are set forth below. If no address is given, the business address is Jupiterstraat 250, 2132 HK Hoofddorp, Netherlands.