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ebi-chebi / ChEBI

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
https://www.ebi.ac.uk/chebi
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Question on identical IUPAC names #4360

Closed paola-scibite closed 1 year ago

paola-scibite commented 1 year ago

Hi,

The following 3-star curated entries share the same IUPAC name, 3-(2-amino-2-carboxyethyl)-1H-indol-1-yl: CHEBI:32731 - 1-tryptophano group CHEBI:32730 - tryptophanyl radical My non-expert understanding is that these are general IUPAC names, rather than Preferred IUPAC Names which should be unique for organic compounds. Could you please confirm if "3-(2-amino-2-carboxyethyl)-1H-indol-1-yl" is a valid name for both CHEBI classes?

Many thanks, Paola

amalik01 commented 1 year ago

We generate IUPAC names using ACD chemsketch and its unable to differentiate between the IUPAC name of a group and a monovalent radical. For example, methyl group (CHEBI:32875) has an IUPAC name called ‘methyl’ and methyl radical (CHEBI:29309) also has an IUPAC name called ‘methyl’.

According to IUPAC, an alkyl group is a group of atoms that results when one hydrogen atom is removed from an alkane. The group is named by replacing the -ane suffix of the parent hydrocarbon with -yl. For example, the CH3 group derived from methane (CH4) results from subtracting one hydrogen atom and is called a methyl group. Alkyl groups are not independent molecules; they are parts of molecules that we consider as a unit to name compounds systematically. Monovalent radicals are also treated in the same way (see RC-81.1.1 https://iupac.qmul.ac.uk/ions/RC811.html)

paola-scibite commented 1 year ago

@amalik01 thank you for explaining that. Best wishes, Paola