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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

Website

http://www.hmdb.ca

Email

Not available

Phone

no phone

Fax

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ZINC Subset Overview

Last updated

2014-03-11

Source catalog size

32,518

Number filtered out

12,078

Upload to PubChem?

No

Purchasability

Not for Sale (Annotated)

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Sample molecules

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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	843	1,569	2,928	5,344	40,513

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 (1148) - 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	0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44	0 1	0 1 2 3 4 5 6 7 8	All	Single Usual Metals All	Single Usual Metals All