UCSF banner
Not-for-sale catalogs

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.

The paper for the TCM Database @ Taiwan is Chen CY-C (2011) TCM Database@Taiwan: The World's Largest Traditional Chinese Medicine Database for Drug Screening In Silico. PLoS ONE 6(1): e15939. doi:10.1371/journal.pone.0015939.

Additional usage notes may be found below the table.
Logo

(click to browse ZINC)

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

PubChem
email 
p.phone
f.fax		 31453252
2011-05-17		15467019 download
3193633
5367313
NYA		 90%:151237
80%:95784
70%:38943
60%:13299
UMBBD
no email 
p.no phone
f.no fax		 1319
2011-12-05		1517 download
172
79
NYA		 90%:714
80%:478
70%:259
60%:158
ChEMBL12
no email 
p.no phone
f.no fax		 1076486
2011-12-19		1223663 download
62410
92843
NYA		 90%:226856
80%:100825
70%:42851
60%:16388
ChEMBL12 10uM
no email 
p.no phone
f.no fax		 238073
2011-12-29		274905 download
15604
3262
NYA		 90%:84333
80%:39982
70%:18913
60%:7531
SMDC Life and Maybridge (building blocks)
no email 
p.no phone
f.no fax		 2451
2012-02-20		2756 download
5
9
NYA		 90%:2285
80%:1985
70%:1510
60%:920
SMDC CDiv Carboxamide
no email 
p.no phone
f.no fax		 4417
2012-02-20		5516 download
205
132
NYA		 90%:2064
80%:1284
70%:831
60%:504
SMDC ChBr Diverse
no email 
p.no phone
f.no fax		 23865
2012-02-20		32099 download
124
2541
NYA		 90%:14293
80%:7678
70%:4174
60%:2159
SMDC CDiv Kinase
no email 
p.no phone
f.no fax		 10000
2012-02-20		11581 download
2
531
NYA		 90%:2358
80%:922
70%:464
60%:267
SMDC ChBr Premium
no email 
p.no phone
f.no fax		 30000
2012-02-20		44774 download
3
3647
NYA		 90%:27406
80%:16307
70%:6889
60%:2358
SMDC Iconix
no email 
p.no phone
f.no fax		 909
2012-02-20		1065 download
45
25
NYA		 90%:749
80%:642
70%:550
60%:446
SMDC MicroSource
no email 
p.no phone
f.no fax		 2160
2012-02-20		3404 download

277
NYA		 90%:1428
80%:1118
70%:836
60%:540
SMDC CDiv Diverse
no email 
p.no phone
f.no fax		 50000
2012-02-21		69194 download
33
1334
NYA		 90%:28491
80%:14405
70%:7214
60%:3264
NPC (NCGC Pharma)
email 
p.phone
f.fax		 2994
2012-03-13		3784 download
133
229
NYA		 90%:2349
80%:1868
70%:1431
60%:929
SMDC Asinex (building blocks)
no email 
p.no phone
f.no fax		 263
2012-04-04		425 download
0
8
NYA		 90%:179
80%:117
70%:77
60%:43
SMDC Life Kinase
no email 
p.no phone
f.no fax		 13010
2012-04-05		16456 download
247
311
NYA		 90%:3572
80%:1745
70%:1015
60%:591
SMDC Pharmakon
no email 
p.no phone
f.no fax		 1600
2012-04-06		2194 download
192
57
NYA		 90%:1167
80%:957
70%:756
60%:524
TTD via PubChem
email 
p.phone
f.fax		 14771
2012-04-19		14372 download
1873
1439
NYA		 90%:7871
80%:5575
70%:3935
60%:2391
MicroSource Spectrum
email 
p.phone
f.fax		 2320
2012-05-09		3618 download
82
85
NYA		 90%:1702
80%:1309
70%:1011
60%:667
FDA-approved drugs (via DSSTOX)
no email 
p.N/A
f.N/A		 1217
2012-07-25		3180 download
163
507
NYA		 90%:976
80%:791
70%:643
60%:480
AmpC non-binders
email 
p.phone
f.fax		 84
2012-07-25		119 download
1
17
NYA		 90%:78
80%:74
70%:64
60%:54
AmpC ligands
email 
p.phone
f.fax		 21
2012-07-25		21 download
0
0
NYA		 90%:16
80%:11
70%:8
60%:6
IUPHAR Database
no email, not a vendor 
p.no phone, not a vend
f.no fax, not a vendor		 3491
2012-10-11		3974 download
250
379
NYA		 90%:2328
80%:1953
70%:1620
60%:1194
Bitter DB
no email 
p.no phone
f.no fax		 580
2012-11-01		686 download
16
40
NYA		 90%:436
80%:363
70%:301
60%:216
IBM Patent Data
email 
p.phone
f.fax		 499997
2012-12-24		736834 download
6659
10593
NYA		 90%:211731
80%:145371
70%:69006
60%:25800
NIH Clinical Collection
email 
p.phone
f.fax		 446
2013-01-15		552 download
23
16
NYA		 90%:389
80%:357
70%:324
60%:272
StreptomeDB
no email 
p.no phone
f.no fax		 2444
2013-01-26		4029 download
511
163
NYA		 90%:1219
80%:935
70%:693
60%:477
Nubbe Natural Products
email 
p.phone
f.fax		 643
2013-01-28		588 download
19
22
NYA		 90%:291
80%:200
70%:140
60%:90
Collaborative Drug Discovery
no email - not a vendor 
p.no phone
f.no fax		 1412817
2013-03-18		1668579 download
13938
120145
NYA		 90%:388174
80%:188373
70%:45371
60%:10082
ChemDB
no email 
p.no phone
f.no fax		 4140778
2013-04-04		3739953 download
116931
691312
NYA		 90%:262144
80%:83180
70%:47891
60%:17644
E. coli Metabolome Database
no email 
p.no phone
f.no fax		 1594
2013-07-19		1976 download
315
121
NYA		 90%:707
80%:435
70%:295
60%:198
Herbal Ingredients Targets
no email 
p.no phone
f.no fax		 531
2013-08-12		802 download
23
64
NYA		 90%:337
80%:268
70%:217
60%:151
Herbal Ingredients In-Vivo Metabolism
no email 
p.no phone
f.no fax		 1270
2013-08-12		663 download
61
27
NYA		 90%:184
80%:133
70%:110
60%:80
Yu Chen 1
email 
p.phone
f.fax		 38023
2013-09-05		51371 download
22
515
NYA		 90%:18461
80%:8081
70%:3574
60%:1192
Yu Chen 3
email 
p.phone
f.fax		 57024
2013-09-05		90779 download
0
600
NYA		 90%:20366
80%:7987
70%:3457
60%:1109
Yu Chen 2
email 
p.phone
f.fax		 57084
2013-09-05		91016 download
1
1462
NYA		 90%:13693
80%:4459
70%:1771
60%:552
NPACT Database
no email 
p.no phone
f.no fax		 1574
2013-09-17		1423 download
93
36
NYA		 90%:773
80%:537
70%:367
60%:209
ChEMBL17
no email 
p.no phone
f.no fax		 1318187
2014-01-20		1583615 download
35359
52293
NYA		 90%:N/A
80%:N/A
70%:0
60%:0
NIH Clinical Collection via PubChem
email 
p.phone
f.fax		 770
2014-01-20		1056 download
35
28
NYA		 90%:648
80%:563
70%:492
60%:396
PDSP via PubChem
email 
p.phone
f.fax		 2871
2014-01-21		4312 download
75
717
NYA		 90%:2464
80%:2169
70%:1764
60%:1215
Prous via PubChem
email 
p.phone
f.fax		 5656
2014-01-21		6814 download
239
530
NYA		 90%:4652
80%:3985
70%:3288
60%:2448
Biocyc via PubChem
noemail 
p.phone
f.fax		 9112
2014-01-22		12529 download
852
627
NYA		 90%:3691
80%:2121
70%:1220
60%:696
KEGG-C via PubChem
not for sale 
p.no phone
f.no fax		 16343
2014-01-23		17116 download
1043
1204
NYA		 90%:7316
80%:4755
70%:2964
60%:1733
KEGG-D via PubChem
no email 
p.no phone
f.no fax		 7624
2014-01-24		6853 download
372
615
NYA		 90%:4260
80%:3346
70%:2587
60%:1749
Leadscope via PubChem
noemail 
p.phone
f.fax		 150331
2014-01-29		186185 download
2605
8149
NYA		 90%:N/A
80%:N/A
70%:14626
60%:6135
Sweetlead
no email 
p.no phone
f.no fax		 9127
2014-01-29		4770 download
2763
248
NYA		 90%:2530
80%:1924
70%:1420
60%:938
The Broad via PubChem
noemail 
p.phone
f.fax		 140695
2014-01-29		147320 download
331
1602
NYA		 90%:N/A
80%:18562
70%:11046
60%:5355
Human Metabolome Database
not for sale 
p.phone
f.not for sale		 41514
2014-03-11		3935 download
15642
366
NYA		 90%:1187
80%:691
70%:396
60%:246
HMDB Plant
not for sale 
p.no phone
f.no fax		 149
2014-03-11		257 download
8
4
NYA		 90%:118
80%:104
70%:91
60%:64
HMDB Drug Metabolites
not for sale 
p.no phone
f.no fax		 947
2014-03-11		1548 download
29
199
NYA		 90%:634
80%:493
70%:404
60%:315
HMDB Microbe
not for sale 
p.no phone
f.no fax		 171
2014-03-11		226 download
11
7
NYA		 90%:109
80%:77
70%:60
60%:50
HMDB Drug
not for sale 
p.no phone
f.no fax		 2462
2014-03-11		3270 download
94
155
NYA		 90%:1578
80%:1233
70%:969
60%:698
HMDB Food
not for sale 
p.no phone
f.no fax		 32518
2014-03-11		40513 download
12078
1148
NYA		 90%:5344
80%:2928
70%:1569
60%:843
HMDB Toxin
not for sale 
p.no phone
f.no fax		 164
2014-03-11		254 download
20
4
NYA		 90%:97
80%:87
70%:77
60%:68
HMDB Endogenous
not for sale 
p.no phone
f.no fax		 29332
2014-03-11		32544 download
11891
1068
NYA		 90%:4306
80%:2393
70%:1285
60%:729
DrugBank-approved
not for sale 
p.phone
f.not for sale		 1491
2014-03-19		1766 download
54
62
NYA		 90%:1140
80%:959
70%:801
60%:600
DrugBank-experimental
not for sale 
p.phone
f.not for sale		 5039
2014-03-19		4751 download
58
227
NYA		 90%:3630
80%:2889
70%:2250
60%:1585
DrugBank-nutriceuticals
not for sale 
p.phone
f.not for sale		 82
2014-03-19		89 download
4
4
NYA		 90%:59
80%:46
70%:38
60%:31
DrugBank-Street Drugs
no email 
p.no phone
f.no fax		 173
2014-03-19		245 download
0
35
NYA		 90%:109
80%:86
70%:63
60%:47
DrugBank-withdrawn
not for sale 
p.phone
f.not for sale		 69
2014-03-19		87 download
3
10
NYA		 90%:65
80%:64
70%:64
60%:60
CSF Metabolome SMPDB
no email 
p.no phone
f.no fax		 428
2014-03-21		485 download
24
13
NYA		 90%:224
80%:145
70%:100
60%:62
Yeast Metabolome
no email 
p.no phone
f.no fax		 2027
2014-03-28		2568 download
95
84
NYA		 90%:648
80%:394
70%:225
60%:135
Kansas
no email 
p.no phone
f.no fax		 0
2014-03-28		7446 download
0
32
NYA		 90%:1582
80%:732
70%:395
60%:223
CMLDBU
no email 
p.no phone
f.no fax		 1629
2014-03-28		1778 download
50
8
NYA		 90%:895
80%:548
70%:329
60%:205
ChEBI
no email 
p.no phone
f.no fax		 34568
2014-04-29		23523 download
2649
1187
NYA		 90%:9151
80%:5754
70%:3493
60%:1963
Urine Metabolome
no email 
p.no phone
f.no fax		 41498
2014-04-29		39085 download
21315
1839
NYA		 90%:7704
80%:4324
70%:2430
60%:1345
Bovine Metabolome
no email 
p.no phone
f.no fax		 7838
2014-04-30		8443 download
1346
343
NYA		 90%:1247
80%:673
70%:385
60%:222
BindingDB.org
none 
p.not for sale
f.not for sale		 474635
2014-05-13		566998 download
12572
9232
NYA		 90%:187526
80%:94066
70%:42445
60%:14109
ChEMBL18
no email 
p.no phone
f.no fax		 1577012
2014-06-17		1577012 download

42028
NYA		 90%:N/A
80%:N/A
70%:0
60%:20766
SMPDB Small Molecule Pathway Database
no email 
p.no phone
f.no fax		 1512
2014-08-08		2094 download
129
137
NYA		 90%:802
80%:518
70%:360
60%:241
KEGG via PubChem
not for sale 
p.no phone
f.no fax		 23967
2014-08-12		21564 download
1415
1703
NYA		 90%:10146
80%:6894
70%:4529
60%:2705
ChEMBL19
no email 
p.no phone
f.no fax		 1404752
2014-08-25		1609835 download
35718
40635
NYA		 90%:N/A
80%:80659
70%:0
60%:20903
Protein Databank
no email 
p.no phone
f.no fax		 18963
2014-10-03		17633 download
508
653
NYA		 90%:11895
80%:8805
70%:6232
60%:3863
ChEMBL DrugStore
no email 
p.no phone
f.no fax		 8233
2015-01-03		10606 download
341
1397
NYA		 90%:6297
80%:4942
70%:3696
60%:2419
SureChEMBL
no email 
p.no phone
f.no fax		 15241444
2015-01-04		1923511 download
2869545
136287
NYA		 90%:N/A
80%:N/A
70%:N/A
60%:N/A
Lipidomics
no email 
p.no phone
f.no fax		 37328
2015-02-12		26419 download
20893
1329
NYA		 90%:2581
80%:1136
70%:513
60%:218
Ambinter Natural Products
contact at ambinter.com 
p.+33 1 83 64 73 54
f.+33 2 38 25 99 65		 32998
2011-12-07		36057 download
4317
2943
NYA		 90%:9495
80%:4268
70%:2364
60%:1255
Frontier Scientific Services BB
customerservice at frontierssi.com 
p.+1 888-577-2734
f.+1 302-266-8296		 18025
2012-01-18		17112 download
2166
675
NYA		 90%:9996
80%:5178
70%:2277
60%:953
Npedia
no email 
p.no phone
f.no fax		 13000
2013-02-22		22151 download
1813
575
NYA		 90%:5293
80%:3726
70%:2458
60%:1315
ChemExper via PubChem
noemail 
p.phone
f.fax		 156258
2014-01-22		23072 download

79
NYA		 90%:8687
80%:4368
70%:2402
60%:1293
eMolecules BB
info at emolecules.com 
p.phone
f.fax		 772078
2014-04-30		762158 download
41661
12300
NYA		 90%:N/A
80%:N/A
70%:N/A
60%:8349
eMoleculesPlus
info at emolecules.com 
p.phone
f.fax		 6860612
2014-06-17		8390130 download
242681
176880
NYA		 90%:N/A
80%:N/A
70%:0
60%:0
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.