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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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tetrapyrrole preferred standard names #421

Open muthuvenkat opened 18 years ago

muthuvenkat commented 18 years ago

There are two IUPAC/IUBMB standard names for the tetrapyrroles with propanoic side chains: 1) the names using ...dioxo-(bilane name)-(prefix)propanoic acid 2) the names using ...(prefix)(2-carboxyethyl)-(bilane name)-dione Both forms appear in the ChEBI "standard name", although for the compounds of interest to RESID CHEBI:15619 (3Z)-phytochromobilin CHEBI:15618 (3Z)-phycoerythrobilin CHEBI:15617 (3Z)-phycocyanobilin CHEBI:17033 biliverdin you seem to have settled on the (2-carboxyethyl)...dione form, which I also prefer. Kirill and I would like to schedule a conference to discuss our approach to these names and synonyms, and deal with the final set including [crypto|phyco]violobilin, aka biliviolin.

JSG

Reported by: jsgaravelli

muthuvenkat commented 18 years ago

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There is a number of other discrepancies between the tatrapyrrole recommendations ("TP"; http://www.chem.qmul.ac.uk/iupac/tetrapyrrole/) and Revised Section F: Natural Products and Related Compounds ("RF"; http://www.chem.qmul.ac.uk/iupac/sectionF/), most notably

spelling "bilin" [TP] vs "biline" [RF] the use of linear tetrapyrrole parents of various degrees of saturation "bilane" [TP] vs "5,10,15,22,23,24-hexahydro-21H-biline" [RF] "bilene-a"　[TP] vs "5,10,22,23-tetrahydro-21H-biline" [RF] "bilene-b" [TP] vs "5,15,22,24-tetrahydro-21H-biline" [RF] "biladiene-ab" [TP] vs "5,23-dihydro-21H-biline" [RF] "biladiene-ac" [TP] vs 10,23-dihydro-22H-biline" [RF]

thus bilirubin can be named either as "8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-3,18-divinylbiladiene-ac-1,19(21H,24H)-dione"

[according to TP] or "2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid" [according to RF]

Kirill

Original comment by: kiri11

jsgaravelli commented 5 years ago

In reviewing the RESID cross-references to ChEBI entries, I noticed that in ChEBI:15671 there is a discrepancy between the structure diagram, and the assigned IUPAC name. In the diagram, three of the four central nitrogens are shown as hydrogenated (formally numbered as 21, 22 and 24), whereas in the name only two nitrogens are indicated as hydrogenated (formally numbered as 21 and 24). I believe that the IUPAC name should be corrected.

amalik01 commented 5 years ago

Hi, Do you have the correct ChEBI ID? ChEBI:15671 is L-tartaric acid and it doesn't have any nitrogens.

jsgaravelli commented 5 years ago

Sorry, numeric dyslexia, That should be ChEBI:15617, (2R,3Z)-phycocyanobilin. You currently have the IUPAC as (2R,3Z)-8,12-bis(2-carboxyethyl)-18-ethyl-3-ethylidene-2,7,13,17-tetramethyl-2,3-dihydrobilin-1,19(21H,24H)-dione. and the structure shown is ...-(21H, 22H, 24H).

amalik01 commented 5 years ago

The IUPAC name is consistent with how these tetrapyrroles are named by IUPAC. See example 5 (biliverdin XIIIα) at https://www.qmul.ac.uk/sbcs/iupac/tetrapyrrole/TP6n7.html#p62 - In this example, three out of the 4 nitrogen's are protonated, but only two of them (21H, 24H) get mentioned in the IUPAC name.