A “Chemical-Structure Map” of the Metabolome


I’ve always struggled to connect the structures of natural products with the biosynthetic pathways that generate them. I recently found a great resource in the Kyoto Encyclopedia of Genes and Genomes (KEGG) which helped me address this problem directly. The figure above is an adaptation of several of their pathway charts most especially that pictured here.

As a database, KEGG strives to be comrehensive; in the figure above, I try to capture the conceptual connections (structure) of metabolism that underlies all the chemistry of life. By explicitely showing core chemical structures that arise out of different pathways, it is my hope that chemists will be able to more readily trace the chemistry (often generated by metabolomic data) to the pathways and organisms that generated them (e.g. the microbiome).



  1. Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.; Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42, D199–D205 (2014).
  2. Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000)


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This work by Eugene Douglass and Chad Miller is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

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