ZINC - A free database for virtual screening

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 represent- atives at a given Tanimoto cutoff
AmpC ligands email p.phone f.fax	21 2008.7	21 0 0 NYA	90%:N/A 80%:N/A 70%:N/A 60%:N/A
AmpC non-binders email p.phone f.fax	84 2008.7	119 0 17 NYA	90%:N/A 80%:N/A 70%:N/A 60%:N/A
BindingDB.org email p.phone f.fax	22500 2008.6	19983 0 202 NYA	90%:6880 80%:3467 70%:1992 60%:1122
CCP W191G binders email p.phone f.fax	43 2008.7	49 0 4 NYA	90%:43 80%:30 70%:22 60%:20
CCP W191G non-binders email p.phone f.fax	17 2008.7	18 0 0 NYA	90%:17 80%:17 70%:14 60%:14
DrugBank-experimental info at drugbank.ca p.phone f.fax	3205 2008.5	4747 621 295 NYA	90%:1708 80%:1314 70%:978 60%:707
DrugBank-nutriceuticals info at drugbank.ca p.phone f.fax	61 2008.5	78 3 4 NYA	90%:45 80%:35 70%:31 60%:25
DrugBank-small molecules info at drugbank.ca p.phone f.fax	4562 2008.5	1488 841 176 NYA	90%:908 80%:772 70%:633 60%:475
FDA-approved drugs (via DSSTOX) no email p.N/A f.N/A	1217 2005-03-01	3180 28 507 NYA	90%:976 80%:791 70%:643 60%:480
Human Metabolome Database info at hmdb.ca p.phone f.fax	5000 2008.5	2561 100 183 NYA	90%:933 80%:548 70%:323 60%:206
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
KEGG no email p.843 884 4911 f.no fax	11415 29.0+/08-1	12429 1932 1371 NYA	90%:5019 80%:3342 70%:2142 60%:1252
KEGG-DRUG noemail p.nophone f.nofax	4779 Feb 08	6607 705 616 NYA	90%:2643 80%:2131 70%:1700 60%:1184
L99A binders email p.phone f.fax	55 2008.7	53 0 12 NYA	90%:N/A 80%:N/A 70%:N/A 60%:N/A
L99A non-binders email p.phone f.fax	65 2008.7	61 0 5 NYA	90%:N/A 80%:N/A 70%:N/A 60%:N/A
L99A/M102Q binders email p.phone f.fax	76 2008.7	73 0 12 NYA	90%:N/A 80%:N/A 70%:N/A 60%:N/A
L99A/M102Q non-binders email p.phone f.fax	20 2008.7	17 0 1 NYA	90%:N/A 80%:N/A 70%:N/A 60%:N/A
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
National Cancer Institute dtpinfo at mail.nih.gov p.no phone f.no fax	260070 Nov 2003	283541 0 94477 NYA	90%:1 80%:1 70%:1 60%:1
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

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 May 6, 2008. bug reports to support at docking.org; comments to comments at docking.org; questions and discussion to blaster-fans at docking.org.