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Synthesis
on Request

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.

Please contact vendor to check delivery times for these compounds. Typically delivery in less than 10 weeks, perhaps much less, but please check!

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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

MicroCombiChem Make-on-demand
info at microcombichem.com 
p.+49-(0)611-962-5284
f.+49-(0)611-962-9265
47
2011-11-22
14 download
33
14
NYA
90%:13
80%:8
70%:4
60%:1
MicroCombiChem BB Make-on-demand
info at microcombichem.com 
p.+49-(0)611-962-5284
f.+49-(0)611-962-9265
607
2011-11-22
716 download
0
524
NYA
90%:355
80%:149
70%:62
60%:30
Focus Synthesis BB Make-on-Demand
focus_synthesis at focussynthesis.com 
p.+1 858 485 5431
f.+1 858 485 5439
1532
2013-05-17
1522 download
68
33
NYA
90%:1184
80%:958
70%:705
60%:455
Zelinsky Institute Make on Demand
sales at zelinsky.com 
p.+1 302 250 4980
f.+1 302 292 8520
2056
2012-06-19
2189 download
2
462
NYA
90%:428
80%:178
70%:83
60%:40
Life Chemicals BB Make-on-Demand
George.Bondar at lifechemicals.com 
p.+1 905 634 5212
f. +1 905 634 4719
4945
2012-10-11
5475 download
1
0
NYA
90%:1802
80%:936
70%:508
60%:212
StruChem BB make-on-demand
service at struchem.com 
p.+86 512 63009836 ext 109
f.+86 512 63006936
7825
2014-04-29
8592 download
329
338
NYA
90%:6047
80%:4082
70%:2050
60%:943
Sphinx Make-on-demand
sales at sphinxscientificlab.com 
p.815 901 8011
f.815 895 6762
23722
2013-04-21
24478 download
334
9547
NYA
90%:13811
80%:5221
70%:2128
60%:929
TimTec BB Make on Demand
info at timtec.net 
p.(302) 292 8500
f.(302) 292 8520
32334
2011-12-14
39213 download
1271
55
NYA
90%:17905
80%:10213
70%:4859
60%:2080
Otava BB Make-to-order
otavaservices at gmail.com 
p.+1 416 549 8030
f.+1 866 881 9921
57433
2015-12-01
6938 download
11916
500
NYA
90%:2189
80%:797
70%:346
60%:135
Innovapharm BB Make on Demand
reag at nbi.com.ua 
p.+38 044 5599572
f.+38 044 4927309
79422
2014-05-06
101988 download
1536
4304
NYA
90%:30056
80%:12836
70%:5398
60%:2148
Aronis BB Make-on-demand
aronis at aronis.ru 
p.+79265780336
f.+7 495 4265336
86278
2013-02-16
75768 download
28991
47959
NYA
90%:5149
80%:852
70%:268
60%:105
Aronis (Make on Request)
aronis at aronis.ru 
p.+79265780336
f.+7 495 4265336
233598
2013-02-19
274498 download
141856
30954
NYA
90%:18537
80%:3071
70%:1009
60%:414
Life Chemicals (Virtual)
George.Bondar at lifechemicals.com 
p.+1 905 634 5212
f.+1 905 634 4719
475970
2015-04-15
539981 download
18258
517549
NYA
90%:N/A
80%:N/A
70%:3096
60%:520
TimTec Make-on-Demand
info at timtec.net 
p.(302) 292 8500
f.(302) 292 8520
531892
2014-05-14
643249 download
36221
962
NYA
90%:117226
80%:45360
70%:17610
60%:5528
Innovapharm Make-on-Demand
reag at nbi.com.ua 
p.+38 044 5599572
f.+38 044 4927309
673505
2013-03-01
786024 download
471068
525359
NYA
90%:N/A
80%:N/A
70%:N/A
60%:N/A
UORSY Make-on-demand
sales at ukrorgsynth.com 
p.+38 044 531 94 97
f.+38 044 531 94 97
978115
2014-09-03
1310640 download
585
227011
NYA
90%:327201
80%:89502
70%:15413
60%:2154
Otava (Virtual)
otavaservices at gmail.com 
p.+1 416 549 8030
f.+1 866 881 9921
2737374
2015-12-01
53765 download
3616
3524
NYA
90%:10784
80%:3488
70%:736
60%:169
Enamine-REAL
enamine at enamine.net 
p.+380 44 537 3218
f.+380 44 537 3253
22120756
2013-02-15
9125817 download
11376
8648897
NYA
90%:151237
80%:57974
70%:15123
60%:2520
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.

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.