UCSF

BindingDB.org

Introduction

BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small\, drug-like molecules. As of March 2014, BindingDB contains 1,009,290 binding data, for 6,589 protein targets and 427,325 small molecules. The paper is: BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK. Nucleic Acids Res. 2007 Jan;35(Database issue):D198-201. Epub 2006 Dec 1. We are grateful to the authors for allowing us to incorporate the molecular structrues of this database in ZINC.

Contact Information

Website
http://www.bindingdb.org
Email
Not available
Phone
not for sale
Fax
not for sale

ZINC Subset Overview

Last updated
2014-05-13
Source catalog size
474,635
Number filtered out
12,572
Upload to PubChem?
No
Purchasability
Not for Sale (Annotated)

Quick Links

Browse
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 7,867 19,906 36,045 53,044 93,345

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 All All All All Single Usual Metals All Single Usual Metals All
SDF All All All All Single Usual Metals All Single Usual Metals All
Flexibase 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 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 0 1 2 3 4 5 6 7 8 9 10 11 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 Single Usual Metals All Single Usual Metals All