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Introduction

AfroDb is a database of natural products from African sources. The paper was published in October 2013 in PLOS One. AfroDb: A Select Highly Potent and Diverse Natural Product Library from African Medicinal Plants by Fidele Ntie-Kang, Denis Zofou, Smith B. Babiaka, Rolande Meudom, Michael Scharfe, Lydia L. Lifongo, James A. Mbah, Luc Meva'a Mbaze, Wolfgang Sippl and Simon M. N. Efange PLOS One 8(10): e78085. doi: 10.1371/journal.pone.0078085 We are grateful to the authors for allowing us to incorporate the molecular structrues of this database in ZINC.

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ZINC Subset Overview

Last updated

2013-11-05

Source catalog size

954

Number filtered out

7

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Purchasability

Collaborations Only

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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	175	282	391	524	885

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 (745) - 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