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Sunday, August 11, 2019

Structure of colibactin elucidated

Structure of colibactin.
Structure elucidation is still a thing. C&EN reported yesterday that a team has published the structure of colibactin (doi:10.1126/science.aax2685), previously not known, despite the major human health impact (cancer). Now, since the article did not seem to have a SMILES, InChI, InChIKey, or even an IUPAC name, I hope I redrew it correctly (see right). The manuscript and supplementary information is, btw, massive in experimental data. Sadly, little of that is FAIR :(

And because there is no open source IUPAC name generator, I cannot provide that either. But I've submitted the structure to PubChem, so hopefully we have the IUPAC name soon.

In the past I would have provided this info in my blog, but we now have Wikidata and Scholia. So, I created a new Wikidata item for the structure, with some initial info, like SMILES, InChI, and InChIKey (using Bacting, of course):


The new publication does not seem to provide experimental physchem properties of colibactin, but before reading the article in detail, I get the impression they simply do not get to synthesize enough of the compound to do such measurements. They do provide NMR and MS data, though. A lot.

Colibactin is one of those compounds a lot was already known about the biology, and there are some 42 articles in Wikidata that discuss the compound and its biological properties, and I linked them to the new item for the compound, and did some additional annotation, giving this nice Scholia page with this topic graph:


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