UCSF

AfroDb Natural Products

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.

Contact Information

Website
http://no web
Email
Not available
Phone
no phone
Fax
no fax

ZINC Subset Overview

Last updated
2013-11-05
Source catalog size
954
Number filtered out
7
Upload to PubChem?
No
Purchasability
Collaborations Only

Quick Links

Browse
Sample molecules
Detailed view
Annotations
Files
Properties
Purchasing
Only from this vendor
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

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