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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.
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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

Asinex
sales at asinex.com 
p.+7 095 780 3411
f.+7 095 780 3419
372187
2006.3
369231 download
125100
67224
NYA
90%:85842
80%:32727
70%:12173
60%:4351
ChemBridge
sales at chembridge.com 
p.858 451 7400
f.858 451 7401
476161
2006.6
430751 download
7737
54157
NYA
90%:130509
80%:41733
70%:14447
60%:5119
ChemDiv
chemdiv at chemdiv.com 
p.858-794-4860
f.858-794-4931
349977
2006.5
445404 download
137686
226899
NYA
90%:2772
80%:2071
70%:1417
60%:882
Chemical Block
orders at chemical-block.com 
p.+7 095 1356343
f.+7 095 1372966
123290
2006.3
119633 download
40980
16873
NYA
90%:51112
80%:27569
70%:13250
60%:5337
Enamine
enamine at enamine.net 
p.+380 44 537 3218
f.+380 44 537 3253
1021826
2006.6
1044816 download
210704
260564
NYA
90%:331628
80%:110069
70%:27044
60%:6230
IBScreen
screen at ibscreen.chg.ru 
p.+7 (095) 788 0651
f.+7 (095) 788 0652
428025
2006.3
536673 download
20010
146927
NYA
90%:100839
80%:40859
70%:16593
60%:5900
Life Chemicals
sales at lifechemicals.com 
p.+1 905 634 5212
f.+1 905 634 4719
200000
2006.5
549442 download
0
222958
NYA
90%:81217
80%:27036
70%:9840
60%:3426
NCI Plated 2007
dtpinfo at mail.nih.gov 
p.no phone
f.no fax
139735
May 07
136784 download
0
101922
NYA
90%:5203
80%:2964
70%:1473
60%:730
Otava
info at otavachemicals.com 
p.(+380 44) 2522389
f.(+380 44) 2522458
196592
2006.5
299848 download
80410
157748
NYA
90%:48324
80%:16168
70%:6265
60%:2323
Pharmeks
sales at pharmeks.com 
p.+7 (095) 702-9648
f.+7 (095) 702-9648
105602
2006.5
155543 download
0
42837
NYA
90%:553
80%:497
70%:410
60%:304
Specs
info at specs.net 
p.+1 401 782 2994
f.410 772 3206
200946
2006.8
248330 download
70581
43833
NYA
90%:1186
80%:836
70%:528
60%:345
Vitas-M
boerrigter at vitasmlab.com 
p.+31 (0) 55 50 500 33
f.+31 (0) 55 50 500 34
243000
2005.6
497393 download
0
137564
NYA
90%:111292
80%:34511
70%:11327
60%:3674
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.