13D Filing: Bay City Capital Fund V, L.P. and Sunesis Pharmaceuticals Inc (SNSS)

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Bay City Capital LLC, a Delaware limited liability company (BCC), hereby files this Amendment
No. 5 (Amendment No. 5) which amends and supplements the Schedule 13D previously filed with the United States Securities and Exchange Commission (the SEC) on April 13, 2009 (the Original 13 D and
amended by Amendment No.1 filed November 3, 2009, Amendment No 2. filed July 1, 2010, Amendment No. 3 filed August 13, 2014 and Amendment No. 4 filed December 22, 2015 (the Schedule 13 D). on behalf of the
Reporting Persons identified in Item 2 of the Schedule pursuant to the Agreement with respect to Schedule 13D attached to the Schedule 13 D as Exhibit 7.1. This Amendment is being filed to reflect changes to the Reporting Persons
ownership of Sunesis Pharmaceuticals, Inc. (the Issuer) as a result of purchases of the Issuers common stock and warrants to purchase common stock by the Reporting Persons in the Issuers underwritten public offering. Except
as supplemented herein, the Schedule 13 D remains in full force and effect. Information given in response to each item shall be deemed incorporated by reference in all other items, as applicable.

BCC is the manager of Bay City Capital Management V LLC (Management V), which is the general partner of Bay City Capital Fund V, L.P., a Delaware
limited partnership (Fund V), and Bay City Capital Fund V Co-Investment Fund, L.P., a Delaware limited partnership (Co-Investment V, and together with Fund V, the Purchasers). BCC is also an advisor to Fund V and
Co-Investment V.

All capitalized terms used and not expressly defined herein have the respective meanings ascribed to such terms in the Schedule 13 D.

ITEM 2. IDENTITY AND BACKGROUND.

Item 2 of the Schedule 13 D is supplemented and amended, as the case may
be, as follows:

Schedule I attached hereto is incorporated herein by reference and amends and restates Schedule 1 of the Schedule 13 D in its entirety.
During the last five years, neither the Reporting Person nor, to the knowledge of the Reporting Person, any of the persons identified on Schedule I to this Amendment: (i) has been convicted in any criminal proceeding (excluding traffic
violations or similar misdemeanors) or (ii) was 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, U.S. federal or state securities laws or finding any violation with respect to such laws.

ITEM 3. SOURCE AND AMOUNT OF FUNDS OR OTHER CONSIDERATION.

Item 3 of the Schedule 13 D is supplemented and
amended, as the case may be, as follows:

The Purchasers acquired certain of the shares of common stock in connection with an underwritten public offering
(the Offering) by the Issuer on October 27, 2017. In the Offering, the Issuer sold a total of 7,500,000 shares of the common stock and accompanying warrants to purchase 3,750,000 shares of Common Stock (collectively, the
Shares) for a purchase price of $2.00 per share.

The Purchasers purchased an aggregate of 600,000 Shares as follows:

Shares Price Paid

Bay City Capital Fund V, L.P.

588,780 * $ $785,040

Bay City Capital Fund V Co-Investment Fund, L.P.

11,220 ** $ 14,960
* Includes 392,520 shares of Common Stock and the accompanying warrants to purchase 196,260 shares of Common Stock.
** Includes 7,480 shares of Common Stock and the accompanying warrants to purchase 3,740 shares of Common Stock.

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