ZINC - A free database for virtual screening

Purchasable bioactives are the purchasable compounds withing annotated catalogs of compounds with biological activity. The annotated catalog does not sell the compounds, but other vendors do. We intersect bioactive chemical space and purchasable chemical space right here. 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. More about ZINC subsets is here. 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
BindingDB.org none p.not for sale f.not for sale	474635 2014-05-13	93345 12572 9232 NYA	90%:53044 80%:36045 70%:19906 60%:7867
Bitter DB no email p.no phone f.no fax	580 2012-11-01	545 16 40 NYA	90%:369 80%:303 70%:250 60%:185
ChEBI no email p.no phone f.no fax	16563 2012-01-26	7457 2072 1119 NYA	90%:3871 80%:2614 70%:1688 60%:1045
ChEMBL DrugStore no email p.no phone f.no fax	8190 2013-02-20	5576 428 1083 NYA	90%:3569 80%:2802 70%:2163 60%:1421
Collaborative Drug Discovery no email - not a vendor p.no phone f.no fax	1412817 2013-03-18	1488435 13938 120109 NYA	90%:433545 80%:172173 70%:42850 60%:7561
DrugBank-approved not for sale p.phone f.not for sale	1408 2012-01-26	1629 85 94 NYA	90%:1040 80%:876 70%:729 60%:547
DrugBank-experimental not for sale p.phone f.not for sale	5046 2012-01-26	4473 897 705 NYA	90%:2303 80%:1816 70%:1401 60%:982
DrugBank-nutriceuticals not for sale p.phone f.not for sale	75 2012-01-26	89 3 10 NYA	90%:53 80%:43 70%:36 60%:29
DrugBank-Street Drugs no email p.no phone f.no fax	172 2012-01-26	218 0 38 NYA	90%:103 80%:81 70%:59 60%:43
DrugBank-withdrawn not for sale p.phone f.not for sale	66 2012-01-26	76 3 1 NYA	90%:56 80%:55 70%:55 60%:52
FDA-approved drugs (via DSSTOX) no email p.N/A f.N/A	1217 2012-07-25	1985 163 361 NYA	90%:795 80%:660 70%:542 60%:400
HMDB Endogenous not for sale p.no phone f.no fax	29332 2014-03-11	6606 11891 1037 NYA	90%:2206 80%:1267 70%:734 60%:439
Human Metabolome Database not for sale p.phone f.not for sale	3176 2013-08-13	2081 439 366 NYA	90%:855 80%:509 70%:316 60%:204
IBM Patent Data email p.phone f.fax	499997 2012-12-24	31340 6659 10752 NYA	90%:18061 80%:10870 70%:5018 60%:2072
IUPHAR Database no email, not a vendor p.no phone, not a vend f.no fax, not a vendor	3491 2012-10-11	2344 250 346 NYA	90%:1514 80%:1280 70%:1075 60%:823
KEGG via PubChem no email p.no phone f.no fax	19960 2011-11-28	10490 2242 1971 NYA	90%:5707 80%:4015 70%:2725 60%:1674
Lipidomics no email p.no phone f.no fax	37328 2015-02-12	4438 20893 1326 NYA	90%:908 80%:438 70%:230 60%:125
NIH Clinical Collection email p.phone f.fax	446 2013-01-15	522 23 9 NYA	90%:386 80%:355 70%:327 60%:272
NPC (NCGC Pharma) email p.phone f.fax	2994 2012-03-13	3277 133 232 NYA	90%:2146 80%:1708 70%:1306 60%:859
Nubbe Natural Products email p.phone f.fax	643 2013-01-28	147 19 22 NYA	90%:91 80%:72 70%:58 60%:47
PDSP via PubChem email p.phone f.fax	2871 2012-05-16	2610 75 671 NYA	90%:1802 80%:1583 70%:1307 60%:915
Prous via PubChem email p.phone f.fax	5487 2012-05-25	2925 498 579 NYA	90%:2205 80%:1929 70%:1663 60%:1294
SMDC Iconix no email p.no phone f.no fax	909 2012-02-20	996 45 14 NYA	90%:713 80%:608 70%:519 60%:420
SMDC Pharmakon no email p.no phone f.no fax	1600 2012-04-06	2176 192 7 NYA	90%:1158 80%:951 70%:751 60%:525
StreptomeDB no email p.no phone f.no fax	2444 2013-01-26	739 511 158 NYA	90%:405 80%:330 70%:250 60%:186
UMBBD no email p.no phone f.no fax	1319 2011-12-05	793 172 104 NYA	90%:460 80%:311 70%:180 60%:112
Npedia no email p.no phone f.no fax	13000 2013-02-22	1710 1813 575 NYA	90%:904 80%:692 70%:529 60%:362

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.

A product of BCIRC, the Bioinfomatics and Chemical Informatics Research Center @ UCSF. Last updated Aug 6, 2009. questions and discussion to zinc-fans at docking.org; bug reports to support at docking.org; any other correspondence to comments at docking.org. Terms of use. Privacy policy.