ZINC Subsets
Popular and user-created subsets are available for download below. 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.
Subset InformationSubset Name
Free Downloads
1: Single structure per chemical entity
2: Multiple tautomeric and protonation states per chemical entity		SQL Selection Criteria
Set#: 1
Size: 643959
Updated: 2005-02-28
By: jji at cgl.ucsf.edu
Browse		lead-like1: SMILES, mol2:1 2 3 4 5 6 7 All sdf:1 2 3 4 5 6 7 All
2: SMILES, mol2:1 2 3 4 5 6 7 8 All sdf:1 2 3 4 5 6 7 8 All
DOCK flexibase:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 All
Purchasing info		and p.xlogp<4 and p.xlogp> -2 and p.mwt < 350 and p.n_h_donors <= 3 and p.n_h_acceptors <= 6 and p.mwt > 150 and c.purchasable = 1
Set#: 2
Size: 49134
Updated: 2005-02-28
By: jji at cgl.ucsf.edu
Browse		fragment-like1: SMILES, mol2:1 sdf:1
2: SMILES, mol2:1 sdf:1
DOCK flexibase:1 2 3 4 All
Purchasing info		and p.xlogp <3 and p.xlogp> -2 and p.mwt <=250 and p.rb<3 and p.n_h_donors < 3 and p.n_h_acceptors<6 and c.purchasable=1
Set#: 3
Size: 2066906
Updated: 2005-03-03
By: jji at cgl.ucsf.edu
Browse		drug-like1: SMILES, mol2:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 All sdf:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 All
2: SMILES, mol2:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 All sdf:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 All
DOCK flexibase:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 All
Purchasing info		and p.xlogp <= 5 and p.mwt <= 500 and p.n_h_donors <= 5 and p.n_h_acceptors <= 10 and c.purchasable=1
Set#: 4
Size: 713314
Updated: 2005-03-03
By: jji at cgl.ucsf.edu
Browse		greasy-leads1: SMILES, mol2:1 2 3 4 5 6 7 8 All sdf:1 2 3 4 5 6 7 8 All
2: SMILES, mol2:1 2 3 4 5 6 7 8 9 All sdf:1 2 3 4 5 6 7 8 9 All
DOCK flexibase:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 All
Purchasing info		and p.xlogp <6 and p.xlogp>2 and p.mwt<350 and c.purchasable=1
Set#: 5
Size: 1659303
Updated: 2004-08-16
By: jji at cgl.ucsf.edu
Browse		big-n-greasy1: SMILES, mol2:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 All sdf:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 All
2: SMILES, mol2:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 All sdf:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 All
DOCK flexibase:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 All
Purchasing info		and p.xlogp<6 and p.xlogp>2 and p.mwt<600 and p.mwt>300 and c.purchasable=1
Set#: 6
Size: 2731838
Updated: 2004-08-16
By: jji at cgl.ucsf.edu
Browse		all-purchasable1: SMILES, mol2:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 All sdf:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 All
2: SMILES, mol2:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 All sdf:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 All
DOCK flexibase:1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 All
Purchasing info		and c.purchasable=1
Set#: 2150
Size: (working)
Updated: 2007-03-26
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		and p.xlogp <3 and p.xlogp> -2 and p.mwt <=250 and p.rb<3 and p.n_h_donors < 3 and p.n_h_acceptors<6 and c.purchasable=1
Set#: 2151
Size: (working)
Updated: 2007-03-28
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and q.sub_id = p.sub_id_fk and q.qury_id = 1631
Set#: 2152
Size: (working)
Updated: 2007-03-28
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and q.sub_id = p.sub_id_fk and q.qury_id = 1631
Set#: 2153
Size: (working)
Updated: 2007-03-28
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and q.sub_id = p.sub_id_fk and q.qury_id = 1631
Set#: 2154
Size: (working)
Updated: 2007-03-28
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and q.sub_id = p.sub_id_fk and q.qury_id = 1631
Set#: 2155
Size: (working)
Updated: 2007-04-16
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and ( c.cat_id = 116 )
Set#: 2156
Size: (working)
Updated: 2007-04-20
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		and p.xlogp<4 and p.xlogp> -2 and p.mwt < 350 and p.n_h_donors <= 3 and p.n_h_acceptors <= 6 and p.mwt > 150 and c.purchasable = 1
Set#: 2157
Size: (working)
Updated: 2007-04-20
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		and p.xlogp<4 and p.xlogp> -2 and p.mwt < 350 and p.n_h_donors <= 3 and p.n_h_acceptors <= 6 and p.mwt > 150 and c.purchasable = 1
Set#: 2158
Size: (working)
Updated: 2007-05-19
By: coward@docking.org
Browse		cyd1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info
Set#: 2159
Size: (working)
Updated: 2007-05-21
By: coward@docking.org
Browse		ZINC029903321: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and q.sub_id = p.sub_id_fk and q.qury_id = 1843
Set#: 2160
Size: (working)
Updated: 2007-05-21
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and q.sub_id = p.sub_id_fk and q.qury_id = 1843
Set#: 2163
Size: (working)
Updated: 2007-05-29
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		and p.xlogp <= 5 and p.mwt <= 500 and p.n_h_donors <= 5 and p.n_h_acceptors <= 10 and c.purchasable=1
Set#: 2164
Size: (working)
Updated: 2007-05-29
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		and p.xlogp <= 5 and p.mwt <= 500 and p.n_h_donors <= 5 and p.n_h_acceptors <= 10 and c.purchasable=1
Set#: 2169
Size: (working)
Updated: 2007-06-14
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		and p.xlogp <= 5 and p.mwt <= 500 and p.n_h_donors <= 5 and p.n_h_acceptors <= 10 and c.purchasable=1
Set#: 2172
Size: (working)
Updated: 2007-06-28
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and ( c.cat_id = 109 )
Set#: 2173
Size: (working)
Updated: 2007-06-28
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and ( c.cat_id = 7 )
Set#: 2174
Size: (working)
Updated: 2007-07-06
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and ( c.cat_id = 2 )and p.mwt >= 0 and p.mwt <= 600 and p.n_h_donors >= 0 and p.n_h_donors <= 6 and p.n_h_acceptors >= 0 and p.n_h_acceptors <= 10
Set#: 2175
Size: (working)
Updated: 2007-07-07
By: coward@docking.org
Browse		2001: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and ( c.cat_id = 2 )and p.mwt >= 0 and p.mwt <= 600 and p.n_h_donors >= 0 and p.n_h_donors <= 6 and p.n_h_acceptors >= 0 and p.n_h_acceptors <= 10
Set#: 2176
Size: (working)
Updated: 2007-07-21
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		and p.xlogp<4 and p.xlogp> -2 and p.mwt < 350 and p.n_h_donors <= 3 and p.n_h_acceptors <= 6 and p.mwt > 150 and c.purchasable = 1
Set#: 2177
Size: (working)
Updated: 2007-08-17
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and q.sub_id = p.sub_id_fk and q.qury_id = 2121
Set#: 2179
Size: (working)
Updated: 2007-08-31
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and ( c.cat_id = 6 )
Set#: 2180
Size: (working)
Updated: 2007-09-04
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		and p.xlogp <3 and p.xlogp> -2 and p.mwt <=250 and p.rb<3 and p.n_h_donors < 3 and p.n_h_acceptors<6 and c.purchasable=1
Set#: 2183
Size: (working)
Updated: 2007-09-07
By: coward@docking.org
Browse		dl400-4501: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		and p.net_charge >= -2 and p.net_charge <= 2 and p.xlogP >= 0 and p.xlogP <= 5 and p.rb >= 4 and p.rb <= 15 and p.mwt >= 400 and p.mwt <= 450 and p.n_h_donors >= 2 and p.n_h_donors <= 5 and c.purchasable = 1
Set#: 2192
Size: (working)
Updated: 2007-10-16
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and ( c.cat_id = 2 ) and q.sub_id = p.sub_id_fk and q.qury_id = 2214
Set#: 2193
Size: (working)
Updated: 2007-10-23
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and q.sub_id = p.sub_id_fk and q.qury_id = 2250
Set#: 2209
Size: (working)
Updated: 2007-10-30
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and q.sub_id = p.sub_id_fk and q.qury_id = 2289
Set#: 2210
Size: (working)
Updated: 2007-10-30
By: coward@docking.org
Browse		zinc_top1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and q.sub_id = p.sub_id_fk and q.qury_id = 2289
Set#: 2212
Size: (working)
Updated: 2007-11-02
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and ( c.cat_id = 4 )
Set#: 2213
Size: (working)
Updated: 2007-11-02
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and ( c.cat_id = 4 )
Set#: 2215
Size: (working)
Updated: 2007-11-09
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and ( c.cat_id = 116 )
Set#: 2216
Size: (working)
Updated: 2007-12-05
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and q.sub_id = p.sub_id_fk and q.qury_id = 2349
Set#: 2217
Size: (working)
Updated: 2007-12-19
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and ( c.cat_id = 110 )
Set#: 2218
Size: (working)
Updated: 2007-12-19
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and ( c.cat_id = 110 )
Set#: 2221
Size: (working)
Updated: 2008-02-06
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and q.sub_id = p.sub_id_fk and q.qury_id = 2519
Set#: 2222
Size: (working)
Updated: 2008-02-07
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info		 and ( c.cat_id = 122 )
Set#: 2223
Size: (working)
Updated: 2008-02-11
By: coward@docking.org
Browse		Not specified1: SMILES, mol2:sdf:
2: SMILES, mol2:sdf:
DOCK flexibase:
Purchasing info

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, files on the line beginning with 1: include a single representation of each substance. Files on the line beginning with a 2: include multiple representations of each substance. This includes multiple protonation states (we aim to sample between pH 5.0 and 9.5) as well as multiple tautomeric forms. ZINC numbers refer to molecules at the substance level, so a single ZINC catalog number may appear multiple times in the 2: files, but only once in the 1: files.

If you are unsure of which database to use, may we suggest the fragment-like database for rapid docking and testing? Once you have parameterized your site and controlled for known binders, moving on to the modestly-sized yet diverse and purchasable lead-like collection is not a bad way to go.

The flexibase format files are only read by the DOCK3.5.54 software program.

Last updated: Jul 18, 2004 by jji at cgl.ucsf.edu.