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.
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:
Tanimoto Cutoff Level | 60% | 70% | 80% | 90% | 100% |
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Number of Representatives | 843 | 1,569 | 2,928 | 5,344 | 40,513 |
We compute the physical properties of each molecule in the subset, and graph them below.
Download Calculated Physical Properties
Format | Reference(pH 7) | Mid(pH 6-8) | High(pH 8-9.5) | Low(pH 4.5-6) | Download Unix |
Download Windows |
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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 |