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Introduction

KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies. A recent paper is: Molecular network analysis of diseases and drugs in KEGG. Kanehisa M. Methods Mol Biol. 2013;939:263-75. doi: 10.1007/978-1-62703-107-3_17. We are grateful to the authors for creating and curating KEGG and thank them for making the structures available via PubChem for incorporation into ZINC. Please note that there are : keggviapc, keggcviapc, keggdviapc. Also, if you are interested in human metabolites only, you may find hmdb interesting.

Contact Information

Website

http://www.genome.jp/kegg/kegg2.html

Email

Not available

Phone

no phone

Fax

no fax

ZINC Subset Overview

Last updated

2013-02-23

Source catalog size

23,967

Number filtered out

1,415

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	1,674	2,725	4,015	5,707	10,490

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 (1971) - correct when the subset was prepared.

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	Not Available	Not Available	Not Available	Not Available