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, Kr├╝ger 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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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 16,388 42,851 100,825 226,856 1,223,663

Physical Property Distributions

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

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MOL2 0 1 2 3 4 5 6 7 8 9 10 0 1 0 1 0 1 Single Usual Metals All Single Usual Metals All
SDF 0 1 2 3 4 5 6 7 8 9 10 0 1 0 1 0 1 Single Usual Metals All Single Usual Metals All
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