UCSF

E. coli Metabolome Database

Introduction

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.

Contact Information

Website
http://www.ecmdb.ca
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Not available
Phone
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ZINC Subset Overview

Last updated
2013-07-19
Source catalog size
1,594
Number filtered out
315
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 198 295 435 707 1,976

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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