Document Format Files
| Seq | Description | Document | Type | Size |
|---|---|---|---|---|
| 1 | FORM S-1 | ds1.htm | S-1 | 2606471 |
| 2 | SEVENTH AMENDED AND RESTATED CERTIFICATE OF INCORPORATION | dex31.htm | EX-3.1 | 123684 |
| 3 | AMENDED AND RESTATED BYLAWS OF THE REGISTRANT, AS CURRENTLY IN EFFECT | dex33.htm | EX-3.3 | 161223 |
| 4 | FIFTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT | dex42.htm | EX-4.2 | 211876 |
| 5 | FORM OF WARRANT TO PURCHASE SHARES OF COMMON STOCK | dex43.htm | EX-4.3 | 43730 |
| 6 | WARRANT TO PURCHASE SHARES OF COMMON STOCK | dex44.htm | EX-4.4 | 57019 |
| 7 | FORM OF WARRANT TO PURCHASE SHARES OF SERIES D PREFERRED STOCK - AS OF 5/25/2006 | dex45.htm | EX-4.5 | 47495 |
| 8 | FORM OF WARRANT TO PURCHASE SHARES OF SERIES D PREFERRED STOCK - AS OF 9/28/2007 | dex46.htm | EX-4.6 | 68476 |
| 9 | WARRANT TO PURCHASE SHARES OF COMMON STOCK ISSUED TO ALEXANDRIA EQUITIES, LLC | dex47.htm | EX-4.7 | 73958 |
| 10 | REGISTRATION RIGHTS AGREEMENT | dex48.htm | EX-4.8 | 67565 |
| 11 | LOAN AND SECURITY AGREEMENT | dex101a.htm | EX-10.1A | 374962 |
| 12 | FIRST AMENDMENT TO LOAN AND SECURITY AGREEMENT | dex101b.htm | EX-10.1B | 41365 |
| 13 | LICENSE AGREEMENT | dex102a.htm | EX-10.2A | 175156 |
| 14 | AMENDMENT NO. 1 TO THE MAXYGEN LICENSE | dex102b.htm | EX-10.2B | 87900 |
| 15 | AMENDMENT NO. 2 TO THE MAXYGEN LICENSE | dex102c.htm | EX-10.2C | 8182 |
| 16 | AMENDMENT NO. 3 TO THE MAXYGEN LICENSE | dex102d.htm | EX-10.2D | 84890 |
| 17 | SIDE LETTER - DATED FEBRUARY 18, 2005. | dex102e.htm | EX-10.2E | 7318 |
| 18 | SIDE LETTER - DATED SEPTEMBER 11, 2007 | dex102f.htm | EX-10.2F | 10991 |
| 19 | SIDE LETTER - DATED SEPTEMBER 24, 2007 | dex102g.htm | EX-10.2G | 11023 |
| 20 | LEASE AGREEMENT | dex108a.htm | EX-10.8A | 368416 |
| 21 | AMENDMENT TO LEASE AGREEMENT - JUNE 1, 2004 | dex108b.htm | EX-10.8B | 14551 |
| 22 | AMENDMENT TO LEASE AGREEMENT - MARCH 9, 2007 | dex108c.htm | EX-10.8C | 71152 |
| 23 | AMENDMENT TO LEASE AGREEMENT - MARCH 31, 2008 | dex108d.htm | EX-10.8D | 167027 |
| 24 | MASTER SECURITY AGREEMENT | dex109.htm | EX-10.9 | 179772 |
| 25 | 2002 STOCK PLAN, AS AMENDED, AND FORM OF STOCK OPTION AGREEMENT | dex1010.htm | EX-10.10 | 248341 |
| 26 | OFFER LETTER - ALAN SHAW | dex1012a.htm | EX-10.12A | 16280 |
| 27 | CHANGE IN CONTROL AGREEMENT - ALAN SHAW | dex1012b.htm | EX-10.12B | 107720 |
| 28 | OFFER LETTER AGREEMENT - ROBERT S. BEUIL | dex1013a.htm | EX-10.13A | 19127 |
| 29 | CHANGE IN CONTROL AGREEMENT - ROBERT S. BREUIL | dex1013b.htm | EX-10.13B | 35450 |
| 30 | SEPARATION AGREEMENT - ROBERT S. BREUIL | dex1013c.htm | EX-10.13C | 56315 |
| 31 | OFFER LETTER AGREEMENT - DOUGLAS T. SHEEHY | dex1014a.htm | EX-10.14A | 23729 |
| 32 | CHANG IN CONTROL AGREEMENT - DOUGLAS T. SHEEHY | dex1014b.htm | EX-10.14B | 108125 |
| 33 | OFFER LETTER AGREEMENT - DAVID L. ANTON | dex1015.htm | EX-10.15 | 19077 |
| 34 | EMPLOYMENT CONTRACT - PETER SEUFER-WASSERTHAL | dex1016.htm | EX-10.16 | 40010 |
| 35 | FORM OF INDEMNIFICATION AGREEMENT | dex1018.htm | EX-10.18 | 42336 |
| 36 | LIST OF SUBSIDIARIES | dex21.htm | EX-21 | 4059 |
| 37 | CONSENT OF INDEPENDENT PUBLIC ACCOUNTING FIRM | dex231.htm | EX-23.1 | 1349 |
| 38 | GRAPHIC | g44003g10k91.jpg | GRAPHIC | 13947 |
| 39 | GRAPHIC | g44003g83z34.jpg | GRAPHIC | 29272 |
| 40 | GRAPHIC | g44003g84f06.jpg | GRAPHIC | 178783 |
| 41 | GRAPHIC | g58802codexis.jpg | GRAPHIC | 4380 |
| 42 | GRAPHIC | g58802g19a05.jpg | GRAPHIC | 6054 |
| 43 | GRAPHIC | g58802g27h39.jpg | GRAPHIC | 2055 |
| 44 | GRAPHIC | g58802g69p79.jpg | GRAPHIC | 5052 |
| Complete submission text file | 0001193125-09-260412.txt | 6118480 |
IRS No.: 710872999
Type: S-1 | Act: 33 | File No.: 333-164044 | Film No.: 091262256
SIC: 2860 Industrial Organic Chemicals
Assistant Director 6

