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Inchi for peptide type bonds


I use Marvin JS and when I import inchi to generate a peptide structure all the amides bond  are converted in enol type bond.

for e.g. InChI=1S/C23H35N9O8S/c1-11(34)32-4-2-3-17(32)23(40)29-14(5-12-7-26-10-

if you generate structure from this inchi it results in the below structure which is incorrect. This is the case foe all the peptide type bonds

peptide bong



Thank you for the report. I dumped the InChI native internal structure and it seems it does not consider any of the carbons at the and of the wiggly bonds as stereo center. My educated guess is that we do something wrong when we clean the molecule during import and identify the affected carbons as unknown tetrahedral stereo centers.

I work on this issue with a high priority, I will get back to you as soon as I find out the actual cause.

Thanks, Istvan

kind regards


Dear Indu,

Thank you again for reporting this issue, it helps a lot to improve our products. I found the root cause, and my guess was right, we invoked the clean functionality with wrong presets inside our InChI import. The fix is ready and it will be released in version 20.15. The fix affects all ChemAxon products, it will solve the issue in MarvinJS as well (more precisely in the underlying webservice, so that the update of your webservice installation will be mandatory to get the fixed functionality)

Best regards,

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