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Introduction

This is a hand crafted subset. Thus the links to browse at the bottom do not YET work. There are two special files associated with this subset.

justification.txt - On each line, there are two ZINC IDs. The first one is the natural product. The second one is the molecule that is included in the subset. Thus the second one is tanimoto 80% or more to the first, or a 10+ atom fragment of the first. If you find a counter example, please let us know so that we can debug!

ZINC ID list - On each line, there are the substance ids that are included in this set.

We first created this subset on Jan 18, 2012. Since this is the first time we have done this, we may have made errors. If you find any problems with this subset, please let us know so that we can put them right. We intend to create a fresh version of this special subset at least twice a year.

General Information

Created By

jji at cgl.ucsf.edu

Critieria

p.mwt <= 500 and p.mwt >= 150 and p.xlogp <= 5 and p.rb <=7 and p.psa < 150 and p.n_h_donors <= 5 and p.n_h_acceptors <= 10

Subset ID

103

ZINC Subset Overview

Last Updated

2013-02-24

Subset Size

101,746

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	60%	70%	80%	90%	100%
Number of Representatives	3,183	6,682	13,068	27,367	101,746

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 (19,319)

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