Download ZINC Subsets

ZINC Database by Vendor
These databases have been provided to us under collaborative agreements with each respective vendor. Molecules in the original catalogs may not appear in ZINC because they do not pass our filters, or they have not been processed yet. ZINC may be used free of charge for research by individuals and institutions. Whereas you are free to share the results of a ZINC search or a screen of molecules from ZINC, you may not redistribute major portions of ZINC without the express written permission of John Irwin. Additional usage notes may be found below the table.

ZINC Database by Vendor

These databases have been provided to us under collaborative agreements with each respective vendor. Molecules in the original catalogs may not appear in ZINC because they do not pass our filters, or they have not been processed yet. ZINC may be used free of charge for research by individuals and institutions. Whereas you are free to share the results of a ZINC search or a screen of molecules from ZINC, you may not redistribute major portions of ZINC without the express written permission of John Irwin. Additional usage notes may be found below the table.

Vendor Information Name Email Phone Fax	Catalog Information Source entries Version/Date	ZINC Information Loaded Filtered Sole source Depleted	Diversity Information Cluster representatives at a given Tanimoto cutoff
ACB Blocks info at acbblocks.com p.+7 095 761 4365 f.+7 095 412 2787	2325 2006.04	2928 143 772 NYA	90%:1223 80%:594 70%:345 60%:199
Acros Organics info at acros.com p.N/A f.+32 14 59 34 34	20916 2006.4	13754 7061 1093 NYA	90%:7093 80%:3572 70%:1552 60%:720
Alfa-Aesar info at alfa.com p.+1 978 521 6300 f.+1 978 521 6350	23920 2005.6	12767 10549 639 NYA	90%:6679 80%:3007 70%:1252 60%:558
AnalytiCon Discovery sales at ac-discovery.com p.+49 (0) 331 2300-300 f.+49 (0) 331 2300-333	14654 2007-01-31	13451 44 11587 NYA	90%:3083 80%:729 70%:209 60%:79
Apollo Scientific sales at apolloscientific.co.uk p.+44 161 406 0505 f.+44 161 406 0506	9451 2005.6	19852 4963 366 NYA	90%:12744 80%:7260 70%:3788 60%:1793
Asinex sales at asinex.com p.+7 095 780 3411 f.+7 095 780 3419	372187 2006.3	322996 125100 39442 NYA	90%:82464 80%:32301 70%:12256 60%:4370
Aurora Feinchemie office at aurora-feinchemie.com p.+43 316 58 67 38 f.+43 316 58 47 44	51082 2006.4	33971 24808 5703 NYA	90%:12311 80%:7145 70%:4097 60%:2051
Bachem sales at bachem.com p.+1 800 634 3183 f.+1 610 239 0800	6470 2005.6	2883 3196 372 NYA	90%:968 80%:363 70%:174 60%:102
ChemBridge sales at chembridge.com p.858 451 7400 f.858 451 7401	420000 2006.6	455439 107189 81949 NYA	90%:82551 80%:34029 70%:13864 60%:5135
ChemDiv chemdiv at chemdiv.com p.858-794-4860 f.858-794-4931	349977 2006.5	414143 137686 226072 NYA	90%:N/A 80%:N/A 70%:N/A 60%:N/A
Chemical Block orders at chemical-block.com p.+7 095 1356343 f.+7 095 1372966	123290 2006.3	108292 40980 15712 NYA	90%:47053 80%:25638 70%:12488 60%:5065
Combi-Blocks sales at combi-blocks.com p.+1 877 525 6257 f.+1 858 635 8991	1141 2005.11	437 695 84 NYA	90%:295 80%:170 70%:101 60%:50
ComGenex info at comgenex.com p.650 246 1470 f.650 244 0795	180000 2006.3	83895 125711 81775 NYA	90%:10180 80%:2875 70%:988 60%:370
Digital Specialty Chemicals sales at digitalchem.com p.+1 603 563 5060 f.+1 603 563 9288	1818 2004.5	475 1379 62 NYA	90%:301 80%:222 70%:160 60%:116
Enamine enamine at enamine.net p.+380 44 537 3218 f.+380 44 537 3253	470000 2006.6	876780 210704 419986 NYA	90%:288905 80%:100460 70%:25945 60%:6140
FDA-approved drugs (via DSSTOX) no email p.N/A f.N/A	1217 2005-03-01	2460 28 316 NYA	90%:931 80%:754 70%:617 60%:462
Frinton sales at frinton.com p.Tel f.Fax	5000 2005.10	1170 197 107 NYA	90%:806 80%:579 70%:366 60%:179
IBScreen screen at ibscreen.chg.ru p.+7 (095) 788 0651 f.+7 (095) 788 0652	342438 2006.3	481177 129802 139622 NYA	90%:97329 80%:41401 70%:17289 60%:6277
Individual Suppliers email p.phone f.fax	100 current	3 0 0 NYA	90%:N/A 80%:N/A 70%:N/A 60%:N/A
Indofine chemical at indofinechemical.com p.+1 908 359 6778 f.+1 908 359 1179	1332 2005.11	1505 18 270 NYA	90%:397 80%:183 70%:101 60%:72
KeyOrganics enquiries at keyorganics.ltd.uk p.+44 1840 212137 f.+44 1840 213712	50000 2004-08-01	32672 0 3821 NYA	90%:17756 80%:10593 70%:5820 60%:2598
Lab molecules email p.phone f.fax	100 current	0 0 0 NYA	90%:N/A 80%:N/A 70%:N/A 60%:N/A
Life Chemicals sales at lifechemicals.com p.+1 905 634 5212 f.+1 905 634 4719	200000 2006.5	170752 0 57415 NYA	90%:35289 80%:16440 70%:7068 60%:2950
LOPAC1280 sales at sial.com p.phone f.fax	1280 2005.10	1507 26 321 NYA	90%:942 80%:797 70%:659 60%:501
Maybridge orders at maybridge.com p.+44 1840 770467 f.+44 1840 770111	59284 2006.5	72766 11158 3750 NYA	90%:44131 80%:25382 70%:11574 60%:4132
MicroSource sales at msdiscovery.com p.+1 (860) 350-8078 f.+1 (860) 354-5300	4000 2004-10	3031 165 23 NYA	90%:1278 80%:991 70%:733 60%:485
Molecular Diversity Preservation International lin at mpdi.org p.+41 61 683 7734 f.+41 61 302 8918	10653 2005.6	14065 2248 2167 NYA	90%:6062 80%:3971 70%:2430 60%:1354
Nanosyn sales at nanosyn.com p.+1 650 853 7030 f.+1 650 853 7031	58587 2004-08-01	61185 14540 6015 NYA	90%:25895 80%:13170 70%:6640 60%:2995
National Cancer Institute dtpinfo at mail.nih.gov p.no phone f.no fax	260071 Nov 2003	284148 0 12890 NYA	90%:80660 80%:42851 70%:22686 60%:11133
Oakwood Chemical sales at oakwoodchemical.com p.+1 803 739 8800 f.+1 803 739 6957	19600 2005.6	15662 2285 3087 NYA	90%:8420 80%:4343 70%:2072 60%:930
Otava info at otavachemicals.com p.(+380 44) 2522389 f.(+380 44) 2522458	196592 2006.5	201833 80410 78825 NYA	90%:34767 80%:13629 70%:5889 60%:2430
Peakdale sales at peakdale.com p.+1 302 838 0420 f.+1 302 838 0421	8548 2006	8123 1622 1738 NYA	90%:3697 80%:1609 70%:712 60%:320
PepTech service at peptechcorp.com p.+1 781 273 5400 +1 7 f.6000	1318 2005.6	1313 183 437 NYA	90%:367 80%:161 70%:58 60%:20
Pharmeks sales at pharmeks.com p.+7 (095) 702-9648 f.+7 (095) 702-9648	105602 2006.5	159432 0 45808 NYA	90%:44407 80%:22459 70%:11526 60%:5170
PubChem email p.phone f.fax	4300000 2006.1	2580343 271411 651993 NYA	90%:N/A 80%:N/A 70%:N/A 60%:N/A
Ryan Scientific sales at ryansci.com p.843 884 4911 f.843 884 5568	59696 2006.5	47929 0 73 NYA	90%:30917 80%:18186 70%:8681 60%:3333
Sigma-Aldrich sales at sigma-aldrich.com p.800-325-3010 f.	295652 2006.5	115595 0 12894 NYA	90%:43633 80%:19722 70%:8804 60%:3634
Specs info at specs.net p.+1 401 782 2994 f.410 772 3206	200946 2006.8	252705 70581 49873 NYA	90%:88244 80%:38726 70%:16823 60%:6606
SynChem sales at synchem.com p.phone f.fax	825 2007	829 13 209 NYA	90%:581 80%:344 70%:230 60%:141
Synthonix info at synthonix.com p.phone f.fax	605 2007	201 398 44 NYA	90%:168 80%:101 70%:68 60%:36
TimTec info at timtec.net p.(302) 292-8500 f.(302) 292-8520	93000 2005.11	262231 19202 17665 NYA	90%:87511 80%:37258 70%:15421 60%:5629
Toslab toslab at toslab.com p.+7 343 3754135 f.+7 343 3754135	15941 2005.6	18211 443 10178 NYA	90%:6740 80%:3823 70%:2339 60%:1414
Tyger sales at tygersci.com p.(888) 329-8990 f.(609) 434-0143	2670 2005.10	3167 150 1401 NYA	90%:1620 80%:987 70%:605 60%:355
Vitas-M boerrigter at vitasmlab.com p.+31 (0) 55 50 500 33 f.+31 (0) 55 50 500 34	243000 2005.6	159513 0 16361 NYA	90%:51954 80%:18619 70%:7040 60%:2602
Adesis info at adesisinc.com p.+1 302 323 4880 f.+1 302 323 4879	300 2007-02-10	267 34 131 NYA	90%:216 80%:119 70%:59 60%:16

The following limits are in effect:

Molecules per mol2 or SDF format file: 100,000
Entries per flexibase file 20,000
Typical size of mol2/sdf/flexibase files: 20 to 100 MB
Number of large files that may be downloaded concurrently: 2

In the downloads above, we offer four formats: SMILES, mol2, SDF, and flexibase formats. Most docking programs we know of use mol2. We urge you to not download Flexibaseunless you are using DOCK3.5.54.

We have generated protonated forms in 3 pH ranges. The reference structure ("ref") is a single representative structure at pH 7. The middle pH range ("mid") contains additional protonated forms obtained by titrating protons with pKa between 5.75 and 8.25. The low pH range ("lo") contains additional protonated forms between pH 4.5-7 and the high pH range ("hi") contains additional protonation forms between pH 7-9.5.

Databases are divided into chunks for easier download. mol2 and sdf slices are 100MB or less uncompressed. Flexibase are 160MB or less uncompressed.

To download all files in the usual pH range (5.75-8.25) use "Usual". To download databases for metalloenzymes use "Metal", which adds the pH range 7-9.5 to usual above. For the entire pH range 4.5-9.5 please use "All".

We also offer tables of Molecular Properties, purchasing information, and Inchi files.

Last updated: Sept 5, 2006 by jji at cgl.ucsf.edu.