ZINC - A free database for virtual screening

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 Click to download and Description	Compounds Click to browse	Last Update	Selection criteria	Only one source	T<.9	T<.8	T<.7	T<.6
lead-like (#1) Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748.	3472461	2010-05-20	p.xlogp < 3.5 and p.mwt < 350 and p.rb <= 7	1490795	215828	124771	35289	10083
fragment-like (#2) Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987	406730	2010-05-19	p.xlogp <=2.5 and p.mwt <=250 and p.rb <= 5	75797	138030	51261	19466	7109
drug-like (#3) Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49.	13441546	2010-06-17	p.xlogp <= 5 and p.mwt <= 500 and p.mwt > 150 and p.rb < 8 and p.psa < 150 and p.n_h_acceptors <= 10	7974651	N/A	N/A	N/A	N/A
all-purchasable (#6) Purchasable chemical space	20669372	2010-06-17		12470677	N/A	N/A	N/A	N/A
everything (#10) All public molecules in ZINC, including around 1M compounds not in subset #6 that may not be available commercially	35125792	2010-06-17		16641986	0	0	0	0
clean-leads (#11) As Subset #1, but without 'yuck' compounds.	1442716	2009-12-11	p.xlogp < 3.5 and p.mwt < 350 and p.rb <= 7	1011096	302965	93832	24787	6500
clean-fragments (#12) As Subset #2, but without 'yuck' compounds.	120727	2009-11-12	p.xlogp <=2.5 and p.mwt <=250 and p.rb <= 5	58814	N/A	N/A	N/A	N/A
clean-drug-like (#13) As Subset #3, but without 'yuck' compounds.	9497542	2009-11-13	p.xlogp <= 5 and p.mwt <= 500 and p.mwt >=150 and p.n_h_donors <= 5 and p.n_h_acceptors <= 10	7973055	569344	149662	35289	8535
leads-now (#21) Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748.	1949828	2010-03-26	p.xlogp < 3.5 and p.mwt < 350 and p.rb <= 7	205617	N/A	N/A	N/A	14673
frags-now (#22) Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987	360453	2010-03-19	p.xlogp <=2.5 and p.mwt <=250 and p.rb <= 5	49113	120976	47717	18779	7021
drugs-now (#23) Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49.	6280787	2009-07-03	p.xlogp <= 5 and p.mwt <= 500 and p.mwt > 150 and p.rb < 8 and p.psa < 150 and p.n_h_acceptors <= 10	2223051	241980	100510	43796	16384
all-now (#26) Immediately purchasable chemical space	9240023	2009-09-08		3245702	N/A	N/A	N/A	N/A
goldilocks (#33) not too big, not too small, not too polar, not too greasy, uncharged, just right	722665	2009-07-08	p.net_charge between -1 and 1 and p.mwt between 200 and 300 and p.xlogp between 1 and 3 and p.rb < 6	50131	N/A	N/A	N/A	N/A
sarah (#37) fragments for model systems	681693	2009-07-08	p.mwt between 30 and 250	295156	N/A	N/A	N/A	N/A
clean CNS permeable (#39) more likely to pass the blood-brain barrier	344596	2009-07-03	p.psa between 0 and 60 and p.mwt between 150 and 400 and p.xlogp between 1.5 and 2.7	215552	95985	36494	12776	4289
flagments (#77) between fragments and leads; as requested by denise	981970	2009-02-24	p.xlogp < 3 and p.mwt < 300 and p.rb < 6	651905	N/A	N/A	N/A	N/A
lugs (#78) between leads and drugs; as suggested by denise	5495242	2009-04-03	((p.xlogp < 4 and p.mwt < 400 and p.rb < 10) AND NOT (p.xlogP < 3 and p.mwt < 350 and p.rb<=7))	2710556	N/A	N/A	N/A	N/A
jens (#79) NHR docking set	1543843	2009-10-26	p.xlogp<5 and p.mwt between 400 and 500	568769	N/A	N/A	N/A	N/A
missingleads (#80) missing greasy leads	601316	2009-10-26	p.xlogp between 4 and 5 and p.mwt between 350 and 400	439644	N/A	N/A	N/A	N/A

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.