The Ecoli Metabolome Database (ECMDB) is a manually curated database of small molecule metabolites found in or produced by Escherichia coli (strain K12, MG1655). The paper is: ECMDB: The E. coli Metabolome Database. Guo AC, Jewison T, Wilson M, Liu Y, Knox C, Djoumbou Y, Lo P, Mandal R, Krishnamurthy R, Wishart DS. Nucleic Acids Res. 2012 Oct 29. [Epub ahead of print] PMID: 23109553 We are grateful to the authors for creating and curating this resource, and for making it available for us to incorporate 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%|
|Number of Representatives||198||295||435||707||1,976|
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
|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|