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Introduction

Zmd is the ZINC Metabolites Database. This contains all metabolites that can currently be purchased. It is based on publically available information.

General Information

Created By

jji@cgl.ucsf.edu

Critieria

c.cat_id in (224,460)

Subset ID

97

ZINC Subset Overview

Last Updated

2013-02-20

Subset Size

5,391

Benign functionality only?

No filtering done

Quick Links

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Sample molecules

Detailed view

Annotations view

Files

Properties

Purchasing

Unique Substances

Unix download

MOL2

SDF

Flexibase [Scripts to download database files to Linux/MacOS]

Windows download

MOL2

SDF

Flexibase [Scripts to download database files to 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	371	612	1,040	1,742	5,391

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
• Purchasing Information - Download strongly advised! Correct when the subset was prepared.
• Substances only sold by one vendor (1,177)

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