PMR commented “The intelligible Chemspider image was hand-drawn by the PNAS authors – I donâ€™t know how it got to Chemspider. (Personally I think itâ€™s pretty awful – I do not like stereo bonds which are rectangular rather than wedges. Why do people use them. And You only have to scale the image to corrupt this info). So we need an Open collection of chemical structures.” In case there is confusion please read the original post…the structure was grabbed from a PDF file (4 Total synthesis highlights (Annu. Rep. Prog. Chem., Sect. B: Org. Chem., 2004, 100, 91) – Royal Society of Chemistry)…it is NOT on ChemSpider. The structure was located by a search using Chemrefer, now on ChemSpider. It was not drawn by us, we’re not responsible for it and, to clarify, I don’t like it either.
Oh, and we do have an Open Collection of chemical structures. The deposition process is under beta-testing and anyone can download the data (we will give away the entire structure collection shortly).
Peter commented that Wikipedia is highly curated. I use it a lot. But, I am cautious…ESPECIALLY with stereochemisty. I’m trying to determine what the ACTUAL taxol structure is. My investigations suggest that one stereocenter is WRONG on the Wikipedia structure. The link to the PubChem record is therefore to the incorrect structure in theory.
Also, the systematic name is not what I would term as anywhere near IUPAC standard: Î²-(benzoylamino)-Î±-hydroxy-,6,12b-bis(acetyloxy)-12-(benzoyloxy)-2a,3,4,4a,5,6,9,10,11,12,12a,12b-dodecahydro-4,11-dihydroxy-4a,8,13,13-tetramethyl-5-oxo-7,11-methano-1H-cyclodeca(3,4)benz(1,2-b)
By the way…the name on Drugbank is 5 beta,20-Epoxy-1,2a,4,7 beta,10 beta,13 alpha-hexahydroxytax-11-en-9-one 4,10-diacetate
2-benzoate 13-ester with (2 R,3S)-N-benzoyl-3-phenylisoserine….hmmm…
I would LOVE this post to get confirmation regarding what the right structure is…is Wikipedia CORRECT or Wrong? I THINK the structure on Drugbank is RIGHT. This DIFFERS from the Wikipedia structure by one stereocenter. Check out the InChIs below:
Compare the STEREO layer at:
and compare the stereo for stereo center 37… one is PLUS and one is MINUS. OOPS!
I’m certainly willing to be wrong but the point is, right now, I am not sure what the right structure. Can anyone out there confirm??? Can someone check “the” highly curated data source and tell us?
Until then I am in full agreement with Peter regarding what Wikipedia SHOULD be “Itâ€™s Open, re-usable, very highly curated, and the first place that students look. That – or a derivative – is where the worldâ€™s chemistry should reside. ” HOWEVER, I am calling for confirmation of the structure and correction if necessary. One of either DrugBank OR PubChem, both linked from Wikipedia, is wrong.
In terms of the comment “That – or a derivative – is where the worldâ€™s chemistry should reside”. I DO agree. We have committed to a wiki-environment for Chemistry. We are presently deciding on the appropriate wiki environment (NOT necessarily MediaWiki) to layer onto ChemSpider. Email exchanges are underway with some of the players in this domain at present – and a sincere thanks to Joerg Wegner for his support on this! With Martin Walker on our advisory group (Walkerma on Wikipedia…a very active player in this domain) we look forward to the best advice and guidance from our collaborators.