UCSF

Znd

ZINC Natural Derivatives - chemically modified natural products, commercially available, based on catalogs ending in nd

General Information

Created By
jji@cgl.ucsf.edu
Critieria
c.cat_id in (533,527)
Subset ID
109

ZINC Subset Overview

Last Updated
2013-02-21
Subset Size
30,793
Benign functionality only?
No filtering done

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MOL2
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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 683 1,273 2,704 7,895 30,793

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 Not Available Not Available Not Available Not Available