UCSF

HMDB Toxin

Introduction

The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. The paper is: Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al., HMDB 3.0. The Human Metabolome Database in 2013. Nucleic Acids Res. 2013. Jan 1;41(D1):D801-7. We are grateful to the authors for creating and curating this database and thank them for allowing us to incorporate its structures in ZINC.

Contact Information

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http://www.hmdb.ca
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ZINC Subset Overview

Last updated
2014-03-11
Source catalog size
164
Number filtered out
20
Upload to PubChem?
No
Purchasability
Not for Sale (Annotated)

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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 68 77 87 97 254

Physical Property Distributions

We compute the physical properties of each molecule in the subset, and graph them below.   Download Calculated Physical Properties
 

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