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Property Subsets
Ready-to-download subsets of ZINC filtered by physical properties are available below. To go to the download page, click on the subset name. To browse sample compounds, click on the number of compounds. Three versions of subsets are available:
  • Standard subsets, numbers 1-10 (for delivery in 1-10 weeks)
  • "clean" subsets, numbers 11-20, in which stricter filtering rules have been applied
  • "immediate availability subsets", numbers 21-30 (for delivery in 7-14 days max)
More about ZINC subsets is here. You can also create your own minisubset. 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.
Subset
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and Description
Compounds
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Last UpdateSelection criteriaOnly one sourceT<.9T<.8T<.7T<.6
 lead-like
(#1)

Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748.

60532872014-09-29p.mwt <= 350 and p.mwt >= 250 and p.xlogp <= 3.5 and p.rb <= 72221528 N/AN/AN/AN/A
 fragment-like
(#2)

Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987

8479092015-02-04p.xlogp <=3.5 and p.mwt <=250 and p.rb <= 5235831 N/AN/A3083710579
 all-purchasable
(#6)

Purchasable chemical space

227248252014-11-285384570 N/AN/AN/A0
 shards
(#7)

Type I binding sites

6351592014-05-16p.mwt < 190122190 13029835304128525422
 everything
(#10)

All public molecules in ZINC, including around 1M compounds not in subset #6 that may not be available commercially

422714522014-11-2412050254 0000
 clean-leads
(#11)

As Subset #1, but without 'yuck' compounds.

45912762014-09-25p.mwt <= 350 and p.mwt >= 250 and p.xlogp <= 3.5 and p.rb <= 71624502 N/AN/AN/A0
 clean-fragments
(#12)

As Subset #2, but without 'yuck' compounds.

16118892014-09-24p.xlogp <=3.5 and p.mwt <=250 and p.rb <= 5249180 N/AN/A06274
 clean-drug-like
(#13)

As Subset #3, but without 'yuck' compounds.

131956092013-11-05p.mwt <= 500 and p.mwt >= 150 and p.xlogp <= 5 and p.rb <=7 and p.psa < 150 and p.n_h_donors <= 5 and p.n_h_acceptors <= 106718992 12351060494226857561
 all-clean
(#16)

As Subset #6, but without 'yuck' compounds.

164038652013-12-187743126 34280340329277267561
 clean-shards
(#17)

Type I binding sites

3259502014-11-24p.mwt < 19045427 N/A2026076163327
 leads-now
(#21)

Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748.

36876212014-06-25p.mwt <= 350 and p.mwt >= 250 and p.xlogp <= 3.5 and p.rb <= 7860514 3226383226381004980
 frags-now
(#22)

Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987

7040412015-02-04p.xlogp <=3.5 and p.mwt <=250 and p.rb <= 5144195 N/A8100609799
 all-now
(#26)

Immediately purchasable chemical space

127825902014-05-012896210 0000
 shards-now
(#27)

Type I binding sites

4247752014-09-24p.mwt < 19060490 N/AN/A123255172
 boutique-frags
(#42)

Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987

27555552013-11-08p.xlogp <=3.5 and p.mwt <=250 and p.rb <= 5899179 N/AN/A100823067
 jfk-drugs
(#43)

Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49.

102922102012-11-27p.mwt <= 500 and p.mwt >= 150 and p.xlogp <= 5 and p.rb <=7 and p.psa < 150 and p.n_h_donors <= 5 and p.n_h_acceptors <= 109037173 12603042850151235041
 all-jfk
(#46)

Purchasable chemical space, no price limit

122178452012-11-2710718336 12098937809126035041
 boutique-shards
(#47)

Type I binding sites, no price limit

806982013-11-08p.mwt < 16020310 1805969302390858

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 (often 30MB compressed, containing 20K to 30K molecules each Flexibase are 200MB 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: Jan 30, 2007 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.