Your Opinion WANTED on how should the structure of Tegaserod be drawn

18 Feb

Those of you who watch this blog know that many of the discussions are about chemical structures, accurate representations on databases and how to “correctly” communicate chemical structures/compounds for the users. So, this is an OPINION question…it’s not an “I have an answer” blog post.

So, Tegaserod has, according, the Dailymed here the structure below:

It can be envisaged as having a trans-orientation but the name on DailyMed doesn’t indicate trans….”3-(5-methoxy-1H-indol-3-ylmethylene)-N-pentylcarbazimidamide”

On Wikipedia here we see the structure below and a systematic name supporting a trans-orientation.

Now there are actually a number of ways to represent Tegaserod and, since there’s no stereochemistry to complicate the molecule, and we are interested in the skeleton per se, we can search on the first part of the InChI on a database like ChemSpider. A search on IKBKZGMPCYNSLU as the first part of the InChI for the structure gives 3 hits. Take a look.I don’t see any real reasons to show the crossbonds for the NH but so be it.

Now, consider that the three hits are E-, Z- and crossbond orientations, and their InChIKeys are as shown below, the results set is indeed expected. My question, based on the structures that you see for Tegaserod, would you prefer to see the compound drawn and how would you expect it to be held in the database. Think about what you would expect to happen in terms of a search. If you drew a cis-form should it retrieve cis and crossed? If you drew crossed should it retrieve cis and trans? etc. Remember, it’s an opinion so no answer is wrong…


Posted by on February 18, 2011 in Computing, Data Quality, InChI


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