UCSF

Zmd

ZINC (primary) Metabolites Database - commercially available. Based on HMDB and BioCyc

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

Browse
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 100%
Number of Representatives Not Available

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 Not Available Not Available Not Available Not Available
MOL2 Not Available Not Available Not Available Not Available
SDF Not Available Not Available Not Available Not Available
Flexibase Not Available Not Available Not Available Not Available