Sec Form 13D Filing - COLUMN GROUP II LP filing for RAPT THERAPEUTICS INC (RAPT) - 2019-11-08

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No.    )*

RAPT THERAPEUTICS, INC.

(Name of Issuer)

Common Stock, $0.0001 par value

(Title of Class of Securities)

75382E 109

(CUSIP Number)

Peter Svennilson

The Column Group II, LP

1700 Owens Street, Suite 500

San Francisco, CA 94158

(415) 865-2050

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

November 4, 2019

(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 §§ 240.13d-1(e), 240.13d-1(f) or 240.13d-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 §240.13d-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, as amended (“Securities Exchange Act”) or otherwise subject to the liabilities of that section of the Securities Exchange Act but shall be subject to all other provisions of the Securities Exchange Act (however, see the Notes).

CUSIP No. 75382E 109

CUSIP No. 75382E 109

CUSIP No. 75382E 109

CUSIP No. 75382E 109

CUSIP No. 75382E 109

CUSIP No. 75382E 109

CUSIP No. 75382E 109

CUSIP No. 75382E 109

CUSIP No. 75382E 109

CUSIP No. 75382E 109

SCHEDULE 13D

Item 1. Security and Issuer

The title and class of securities to which this Statement on Schedule 13D (this “Schedule 13D”) relates is the common stock, par value $0.0001 per share (the “Common Stock”), of RAPT Therapeutics, Inc., a Delaware corporation (the “Issuer”). The principal executive office of the Issuer is located at 561 Eccles Avenue, South San Francisco, CA 94080.

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) This Schedule 13D is being filed by (i) The Column Group II, LP, a Delaware limited partnership (“TCG II LP”), (ii) The Column Group II GP, LP, a Delaware limited partnership (“TCG II GP”), (iii) The Column Group II Management LP, a Delaware limited partnership (“TCGM II LP”), (iv) Ponoi Capital, LP, a Delaware limited partnership (“Ponoi LP”), (v) Ponoi Management, LLC, a Delaware limited liability company (“Ponoi LLC”), (vi) Ponoi Capital II, LP, a Delaware limited partnership (“Ponoi II LP”), (vii) Ponoi II Management, LLC, a Delaware limited liability company (“Ponoi II LLC”) and (viii) Peter Svennilson, David V. Goeddel and Tim Kutzkey (collectively referred to as the “Managing Partners”). Mr. Svennilson and Mr. Goeddel are the Managing Partners of TCG II GP and TCGM II LP. Mr. Svennilson, Mr. Goeddel and Mr. Kutzkey are the Managing Partners of Ponoi LLC and Ponoi II LLC. Each of the Managing Partners, TCG II LP, TCG II GP, TCGM II LP, Ponoi LP, Ponoi LLC, Ponoi II LP and Ponoi II LLC are sometimes hereinafter referred to individually as a “Reporting Person,” and, collectively, as the “Reporting Persons.”

(b) The principal executive offices of TCG II LP, TCG II GP, TCGM II LP, Ponoi LP, Ponoi LLC, Ponoi II LP and Ponoi II LLC and the business address of each of the Managing Partners, is 1700 Owens Street, Suite 500, San Francisco, California 94158.

(c) The principal business of each of TCG II LP, Ponoi LP and Ponoi II LP is making venture capital investments. TCGM II LP’s principal business is managing entities that make venture capital investments. TCG II GP’s principal business is acting as general partner of TCG II LP. Ponoi LLC’s principal business is acting as general partner of Ponoi LP. Ponoi II LLC’s principal business is acting as general partner of Ponoi II LP. Each of Mr. Svennilson’s and Mr. Goeddel’s principal business is acting as a managing partner of TCG II GP, TCGM II LP, Ponoi LLC and Ponoi II LLC and of The Column Group GP, LP and The Column Group III GP (“TCG III GP”), LP, affiliates of the Reporting Persons. Mr. Kutzkey’s principal business is acting as a managing partner of Ponoi LLC, Ponoi II LLC and TCG III GP.

(d) During the past five years, none of the Reporting Persons has been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors).

(e) During the past five years, none of the Reporting Persons was a party to a civil proceeding of a judicial or administrative body of competent jurisdiction as a result of which such person 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 of finding any violation with respect to such laws.

(f) Mr. Svennilson is a citizen of Sweden, and Mr. Goeddel and Mr. Kutzkey are citizens of the United States.

Item 3. Source and Amount of Funds or Other Consideration

Effective upon the closing of the Issuer’s initial public offering (the “IPO”) which occurred on November 4, 2019 (the “IPO Closing”), each share of the Issuer’s Series A Preferred Stock, Series B Preferred Stock, Series C Preferred Stock and Series C-2 Preferred Stock converted into approximately 0.166 shares of the Issuer’s Common Stock (on an as-adjusted basis, after giving effect to the 1-for-6 reverse stock split of the Issuer’s Common Stock effected on July 19, 2019). Unless otherwise noted herein, all shares of Common Stock and per share amounts have been adjusted to reflect the reverse stock split.

In July 2014, TCG II LP purchased certain preferred shares of Flexus Biosciences, Inc. (“Flexus”). In April 2015, Flexus contributed and assigned to the Issuer certain of its assets and rights in exchange for Series A Preferred Stock of the Issuer (the “Series A Shares”). Flexus immediately distributed the Series A Shares to its preferred stockholders, including 2,681,963 Series A Shares distributed to TCG II LP, and was subsequently acquired by a third party. The fair market value of the Series A Shares distributed to TCG II LP at the time of distribution was approximately $2,681,963. In April 2015, TCG II LP purchased an aggregate of 12,100,000 shares of Series A Preferred Stock (the “Series A Shares”) for an aggregate purchase price of $12,100,000. In April 2016, TCG II LP purchased an aggregate of 7,000,000 shares of Series B Preferred Stock (the “Series B Shares”) for an aggregate purchase price of $14,000,000. In December 2017, TCG II LP purchased an aggregate of 4,362,050 shares of Series C Preferred Stock (the “Series C Shares”) for an aggregate purchase price of $10,000,000 and Ponoi LP purchased an aggregate of 8,724,100 Series C Shares for an aggregate purchase price of $20,000,000. In December 2018, Ponoi LP purchased an aggregate of 872,410 shares of Series C-2 Preferred Stock (the “Series C-2 Shares” and, together with the Series A Shares, the Series B Shares and the Series C Shares, the “Preferred Stock”) for an aggregate purchase price of $2,000,000 and Ponoi II LP purchased an aggregate of 872,410 Series C-2 Shares for an aggregate purchase price of $2,000,000.

Additionally, TCG II LP purchased 625,000 shares of Common Stock as part of the Issuer’s IPO for an aggregate purchase price of $7,500,000. Upon the IPO Closing, each share of Preferred Stock automatically converted into approximately 0.166 shares of Common Stock. TCG II LP received an aggregate of 4,357,333 shares of Common Stock upon conversion, Ponoi LP received an aggregate of 1,599,417 shares of Common Stock upon conversion and Ponoi II LP received an aggregate of 145,401 shares of Common Stock upon conversion.

As consideration for Mr. Goeddel’s service as interim chief executive officer of the Issuer between May 2015 and August 2015, in June 2015, the Issuer granted TCGM II LP 50,000 shares of Common Stock for which no consideration was paid. The fair market value of these shares at the time of grant was approximately $51,000.

TCG II LP, Ponoi LP and Ponoi II LP received the funds used to purchase each entity’s respective shares of Preferred Stock and/or Common Stock noted above from capital contributions made to each entity by their respective partners for investment purposes.

Item 4. Purpose of Transaction

TCG II LP, TCG II GP, TCGM II LP, Ponoi LP, Ponoi II LP, Mr. Goeddel, Mr. Svennilson and Mr. Kutzkey acquired the aforementioned Preferred Stock and Common Stock for investment purposes with the aim of increasing the value of their investments in the Issuer.

Except as set forth in Item 6 below, none of the Reporting Persons have a present plan or proposal that relates to or would result in any of the actions specified in clauses (a) through (j) of Item 4 of Schedule 13D. However, each of the Reporting Persons reserves the right to propose or participate in future transactions which may result in one or more of such actions, including but not limited to, an extraordinary corporate transaction, such as a merger, reorganization, or liquidation, sale of a material amount of assets of the Issuer or its subsidiaries, or other transactions which might have the effect of causing the Common Stock to become eligible for termination of registration under Section 12(g) of the Securities Exchange Act of 1934, as amended. The Reporting Persons also retain the right to change their investment intent at any time, to acquire additional shares of Common Stock or other securities of the Issuer from time to time, or to sell or otherwise dispose of all or part of the Common Stock beneficially owned by them (or any shares of Common Stock into which such securities are converted) in any manner permitted by law. The Reporting Persons may engage from time to time in ordinary course transactions with financial institutions with respect to the securities described herein.

Item 5. Interest in Securities of the Issuer

(a) As of the date hereof, TCG II LP directly holds 4,982,333 shares of Common Stock, representing 23.4% of the Issuer’s outstanding Common Stock. As the general partner of TCG II LP, TCG II GP beneficially owns an aggregate of 4,982,333 shares of Common Stock, representing 23.4% of the Issuer’s outstanding Common Stock. TCGM II LP directly holds 50,000 shares of Common Stock, representing 0.2% of the Issuer’s outstanding Common Stock. Ponoi LP directly holds 1,599,417 shares of Common Stock, representing 7.5% of the Issuer’s outstanding Common Stock. As the general partner of Ponoi LP, Ponoi LLC beneficially owns an aggregate of

1,599,417 shares of Common Stock, representing 7.5% of the Issuer’s outstanding Common Stock. Ponoi II LP directly holds 145,401 shares of Common Stock, representing 0.7% of the Issuer’s outstanding Common Stock. As the general partner of Ponoi II LP, Ponoi II LLC beneficially owns an aggregate of 145,401 shares of Common Stock, representing 0.7% of the Issuer’s outstanding Common Stock. Mr. Svennilson, beneficially owns 6,777,151 shares of Common Stock, representing 31.8% of the Issuer’s outstanding Common Stock, which consists of 6,777,151 shares of Common Stock that Mr. Svennilson beneficially owns as a Managing Partner of TCG II GP, TCGM II LP, Ponoi LLC and Ponoi II LLC. Mr. Goeddel beneficially owns 6,777,151 shares of Common Stock, representing 31.8% of the Issuer’s outstanding Common Stock, which consists of 6,777,151 shares of Common Stock that Mr. Goeddel beneficially owns as a Managing Partner of TCG II GP, TCGM II LP, Ponoi LLC and Ponoi II LLC. Mr. Kutzkey beneficially owns 1,744,818 shares of Common Stock, representing 8.2% of the Issuer’s outstanding Common Stock, which consists of 1,744,818 shares of Common Stock that Mr. Kutzkey beneficially owns as a Managing Partner of Ponoi LLC and Ponoi II LLC.

The percentages set forth in this Item 5 and in the cover page for each Reporting Person are based on the 21,279,943 outstanding shares of Common Stock as of November 4, 2019, as disclosed in the Issuer’s final prospectus dated October 30, 2019, as file d with the Securities and Exchange Commission (the “SEC”) on November 1, 2019, which assumes no exercise of the underwriters’ option to purchase up to 450,000 additional shares.

(b) TCG II LP has sole voting and dispositive control over 4,982,333 shares of Common Stock, TCGM II LP has sole voting and dispositive control over 50,000 shares of Common Stock, Ponoi LP has sole voting and dispositive control over 1,599,417 shares of Common Stock and Ponoi II LP has sole voting and dispositive control over 145,401 shares of Common Stock. None of the other Reporting Persons own any securities of the Issuer directly. TCG II GP, as general partner of TCG II LP, shares the power to direct the voting and disposition of the 4,982,333 shares owned by TCG II LP and may be deemed to beneficially own the shares owned by TCG II LP. Ponoi LLC, as general partner of Ponoi LP, shares the power to direct the voting and disposition of the 1,599,417 shares owned by Ponoi LP and may be deemed to beneficially own the shares owned by Ponoi LP. Ponoi II LLC, as general partner of Ponoi II LP, shares the power to direct the voting and disposition of the 145,401 shares owned by Ponoi II LP and may be deemed to beneficially own the shares owned by Ponoi II LP. By virtue of their positions as managing partners of TCG II GP and TCGM II LP, each of Mr. Svennilson and Mr. Goeddel may be deemed to share the power to direct the voting and disposition of the 4,982,333 shares owned by TCG II LP and the 50,000 shares owned by TCGM II LP and may be deemed to beneficially own the shares owned by such entities. By virtue of their positions as managing partners of Ponoi LLC and Ponoi II LLC, each Managing Partner may be deemed to share the power to direct the voting and disposition of the 1,599,417 shares owned by Ponoi LP and the 145,401 shares owned by Ponoi II LP and may be deemed to beneficially own the shares owned by Ponoi LP and Ponoi II LP.

(c) Except as set forth herein, none of the Reporting Persons has effected any transactions in shares of the Issuer’s Common Stock during the last 60 days.

(d) No other person is known to have the right to receive or the power to direct the receipt of dividends from, or any proceeds from the sale of, the shares of Common Stock beneficially owned by any of the Reporting Persons.

(e) Not applicable.

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

The Issuer, TCG II LP, Ponoi LP, Ponoi II LP and certain other investors are party to an amended and restated investors’ rights agreement (the “Investors’ Rights Agreement”), dated December 18, 2018, giving such investors the right to demand that the Issuer file a registration statement or request that the investors’ shares of Common Stock be covered by a registration statement that the Issuer otherwise files. In addition to the registration rights, the Investors’ Rights Agreement provides for certain information rights and a right of first offer. The provisions of the Investors’ Rights Agreement terminated upon the IPO Closing, other than the registration rights, which will terminate upon the earlier of (i) five years after the IPO Closing, (ii) with respect to each investor, the date when such investor (A) can sell all of its securities pursuant to Rule 144 of the Securities Act of 1933, as amended, or (B) holds one percent (1%) of less of the Issuer’s outstanding Common Stock and all Registrable Securities, as defined in the Investors’ Rights Agreement, can be sold in any three (3) month period without registration in compliance with Rule 144 or (iii) after the consummation of a Liquidation Event, as defined in the Investors’ Rights Agreement. This summary description does not purport to be complete, and is qualified in its entirety by the Amended and Restated Investors’ Rights Agreement, a copy of which is filed as Exhibit 10.1 to the Issuer’s Registration Statement on Form S-1 filed with the SEC on July 5, 2019 (the “S-1”) and is incorporated herein by reference.

Mr. Goeddel, in his capacity as a director of the Issuer, and along with the other directors of the Issuer, entered into an indemnification agreement with the Issuer providing for indemnification to the fullest extent permitted by applicable law and the Issuer’s amended and restated bylaws. These indemnification agreements provide, among other things, that the Issuer will indemnify its directors and officers for certain expenses, including damages, judgments, fines, penalties, settlements and costs and attorneys’ fees and disbursements, incurred by a director in any claim, action, or proceeding arising in his or her capacity as a director or officer of the Issuer or in connection with service at the Issuer’s request for another corporation or entity. The indemnification agreements also provide for procedures that will apply in the event that a director makes a claim for indemnification. This summary description does not purport to be complete, and is qualified in its entirety by the Form of Indemnification Agreement, a copy of which is filed as Exhibit 10.8 to Amendment No. 1 to the S-1 filed with the SEC on July 22, 2019 and is incorporated herein by reference.

The Issuer, along with its directors and executive officers and substantially all of its other stockholders, including the Reporting Persons, have agreed with the underwriters for the IPO that, for a period of 180 days following October 30, 2019, they will not (i) directly or indirectly, offer, pledge, sell, contract to sell, sell any option or contract to purchase, purchase any option or contract to sell, grant any option, right or warrant to purchase or otherwise transfer or dispose of any shares of the Common Stock (including, for the Issuer’s directors and officers, any shares issued in the IPO or other issuer-directed shares) or any securities convertible into or exercisable or exchangeable for the Common Stock, whether now owned or later acquired or with respect to which they have or later acquire the power of disposition, or exercise any right with respect to the registration of any of such securities, or file, cause to be filed or cause to be confidentially submitted any registration statement in connection therewith or (ii) enter into any swap or any other agreement or any transaction that transfers, in whole or in part, directly or indirectly, the economic consequence of ownership of any such securities, whether any such swap or transaction is to be settled by delivery of the Common Stock or other securities, in cash or otherwise, in each case subject to specified exceptions. The representatives of the underwriters, on behalf of the underwriters, may, in their sole discretion, at any time without prior notice, release all or a portion of the Common Stock and other securities subject to the lock-up agreement described above from the restrictions in any such agreement. This summary description does not purport to be complete, and is qualified in its entirety by the Form of Lock-up attached as Exhibit B to the Underwriting Agreement, a copy of which is filed as Exhibit 1.1 to Amendment No. 3 to the S-1 filed with the SEC on October 22, 2019 and is incorporated herein by reference.

Item 7. Material to be filed as Exhibits

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.