UCSF

ChEBI

Introduction

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on small chemical compounds. The paper is: The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, Steinbeck C. Nucleic Acids Res. 2013 Jan;41(Database issue):D456-63. doi: 10.1093/nar/gks1146. Epub 2012 Nov 24. We are grateful to the authors for creating and maintaining this resource and for allowing us to incorporate its structures in ZINC.

Contact Information

Website
http://www.ebi.ac.uk/chebi/
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ZINC Subset Overview

Last updated
2014-04-29
Source catalog size
34,568
Number filtered out
2,649
Upload to PubChem?
No
Purchasability
Not for Sale (Annotated)

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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 1,963 3,493 5,754 9,151 23,523

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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