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Introduction

ChEMBL is the medicinal chemistry database available from https://www.ebi.ac.uk/chembl. The paper is: The ChEMBL bioactivity database: an update. Bento AP, Gaulton A, Hersey A, Bellis LJ, Chambers J, Davies M, Krüger FA, Light Y, Mak L, McGlinchey S, Nowotka M, Papadatos G, Santos R, Overington JP. Nucleic Acids Res. 2014 Jan;42(Database issue):D1083-90. doi: 10.1093/nar/gkt1031. Epub 2013 Nov 7. We are grateful to the authors for creating and maintaining this resource and for allowing us to incorporate its structures into ZINC. ChEMBL is made available under the CC-BY-CA license, and correspondingly, all derived versions of ChEMBL via ZINC are freely available. CC-BY-SA license

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https://www.ebi.ac.uk/chembl/

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ZINC Subset Overview

Last updated

2014-08-25

Source catalog size

1,404,752

Number filtered out

35,718

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Purchasability

Not for Sale (Annotated)

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Sample molecules

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Unix download

mol2 unix

SDF unix

Flexibase unix [Scripts to download database files on Linux and MacOS]

Win download

mol2 windows

SDF windows

Flexibase windows [Scripts to download database files on Windows]

Chemical Diversity and Clustering

We assess the chemical diversity of a subset by clustering the molecules. First, we sort ligands by increasing molecular weight. Then, we use the SUBSET 1.0 algorithm ( Voigt JH, Bienfait B, Wang S, Nicklaus MC. JCICS, 2001, 41, 702-12) to progressively select compounds that differ from those previously selected by at least the Tanimoto cutoff, using ChemAxon default fingerprints. The resulting representatives have two interesting properties:

• 1) Each representative differs from all the others by at least the Tanitmoto cutoff and
• 2) All the molecules in the subset are within the Tanimoto cutoff of at least one representative.

Thus the representatives can be said to "cover" the chemical space of the subset at a given Tanimoto level. N/A indicates that clustering is pending.

Tanimoto Cutoff Level	60%	70%	80%	90%	100%
Number of Representatives	20,903	0	80,659	0	1,609,835

Physical Property Distributions

We compute the physical properties of each molecule in the subset, and graph them below.   Download Calculated Physical Properties
 

Tab-delimited information files

• Calculated Physical Properties
• Source Catalog Information - Download strongly advised! This information changes rapidly.
• Substances only available from here (40635) - correct when the subset was prepared.

Ready-to-dock molecular files

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Format	Reference(pH 7)	Mid(pH 6-8)	High(pH 8-9.5)	Low(pH 4.5-6)	Download Unix	Download Windows
SMILES	All	All	All	All
MOL2	0 1 2 3 4 5 6 7 8 9 10 11 12 13	0 1 2	0 1 2	0 1	Single Usual Metals All	Single Usual Metals All
SDF	0 1 2 3 4 5 6 7 8 9 10 11 12 13	0 1 2	0 1 2	0 1	Single Usual Metals All	Single Usual Metals All
Flexibase	Not Available	Not Available	Not Available	Not Available