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Introduction

NuBBE: research for the development and sustainable use of the biodiversity The paper is: Valli M1, dos Santos RN, Figueira LD, Nakajima CH, Castro-Gamboa I, Andricopulo AD, Bolzani VS. Development of a natural products database from the biodiversity of Brazil. J Nat Prod. 2013 Mar 22;76(3):439-44. doi: 10.1021/np3006875. Epub 2013 Jan 18. We are grateful to the authors for creating and curating this database and thank them for allowing us to incorporate its structures in ZINC.

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http://nubbe.iq.unesp.br

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ZINC Subset Overview

Last updated

2013-02-22

Source catalog size

643

Number filtered out

19

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No

Purchasability

Not for Sale (Annotated)

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mol2 unix

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Flexibase unix [Scripts to download database files on Linux and MacOS]

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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	47	58	72	91	147

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 (22) - correct when the subset was prepared.

Ready-to-dock molecular files

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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