UCSF

ChemDB

Introduction

ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. (as of March 2014) The paper is: Chen, J. H., Linstead, E., Swamidass, S. J., Wang, D. & Baldi, P. ChemDB update-full-text search and virtual chemical space. Bioinformatics 23, 2348-2351 (2007). We are grateful to the authors for creating and maintaining this resouce, and for allowing us to incorporate its structures into ZINC.

Contact Information

Website
http://cdb.ics.uci.edu
Email
Not available
Phone
no phone
Fax
no fax

ZINC Subset Overview

Last updated
2013-04-04
Source catalog size
4,140,778
Number filtered out
116,931
Upload to PubChem?
No
Purchasability
Not for Sale (Annotated)

Quick Links

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Sample molecules
Detailed view
Annotations
Files
Properties
Purchasing
Only from this vendor
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 17,644 47,891 83,180 262,144 3,739,953

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

Ready-to-dock molecular files

More about this.
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 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 0 1 2 0 1 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 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 0 1 2 0 1 0 1 Single Usual Metals All Single Usual Metals All
Flexibase Not Available Not Available Not Available Not Available