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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.
select subset_id, description, subtype, selection_criteria, created_by, last_updated, actual_size,comment from subset where subtype= 0 or subtype=3 order by subset_id
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and Description
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Last UpdateSelection criteriaOnly one sourceT<.9T<.8T<.7T<.6

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.