SCHEDULE 13D
Item 1. Security and Issuer
This Amendment
No. 1 (the “Amendment”) supplements and amends the Schedule 13D relating to shares of common stock, par value $0.0001 per share (the “Common Stock”), of RAPT Therapeutics, Inc., a Delaware corporation (the
“Issuer”) that was filed with the Securities and Exchange Commission (the “SEC”) on November 8, 2019 (the “Original Statement”). Only those items that are reported are hereby amended; all other items reported in
the Original Statement remain unchanged. Capitalized terms contained herein but not otherwise defined shall have the meanings ascribed to such terms in the Original Statement. Information given in response to each item shall be deemed incorporated
by reference in all other items as applicable.
This Amendment relates to the Issuer’s sale of 2,500,000 shares of its Common Stock as disclosed in
the Issuer’s final prospectus dated February 6, 2020, as filed with the SEC on February 7, 2020 (the “Final Prospectus”) which resulted in an increase in the aggregate number of shares of the Issuer’s Common Stock
outstanding and a decrease in the percentage of the Issuer’s outstanding Common Stock beneficially owned by the Reporting Persons.
Item 5.
Interest in Securities of the Issuer
Item 5(a) of the Original Statement is hereby amended and restated in its entirety as follows:
(a) As of the date hereof, TCG II LP directly holds 4,982,333 shares of Common Stock, representing 20.5% 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 20.5% 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 6.6% 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 6.6% of the Issuer’s outstanding Common Stock. Ponoi II LP directly holds 145,401 shares of Common Stock, representing 0.6% 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 0.6% of the Issuer’s outstanding Common Stock. Mr. Svennilson, beneficially owns 6,777,151 shares of Common Stock, representing 27.9%
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 27.9% 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 7.2% 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 24,329,584 outstanding shares of Common Stock as of February 11, 2020, as disclosed in the Final Prospectus, which assumes no exercise of the underwriters’ option to purchase up to 375,000 additional shares.