Lipid A structure too specific

ebi-chebi / ChEBI

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.

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Lipid A structure too specific #3246

Open dosumis opened 7 years ago

dosumis commented 7 years ago

http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:47040

Lipid A ChEBI ID CHEBI:47040 Definition The glycolipid moiety of bacterial lipopolysaccharide.

Textual def is fine. Structure is true for only some lipid A

While this is correct for lipid A in E.coli it is not true in many other bacteria, which can have 4 or 5 acyl chains rather than 6. Helicobacter pylori has 4 acyl chains, see PMID 22216004, in Bacteroides thetaiotaomicron it has 5 acyl chains, see PMID 20974832.

Perhaps better to treat 'lipid A' as a biological role and have separate entries with attached structures for varients.

G-Owen commented 7 years ago

Hi David,

Thanks for the information. Our knowledge of these things is clearly very limited!

I guess that renaming CHEBI:47040 from lipid A to lipid A (E. coli) is not on, as there will be a number of users who are linking to it in the belief that it is a generic entity.

I am considering: a) Deleting the structure for Lipid A, CHEBI:47040 b) Merging CHEBI:47040 with CHEBI:25051 Lipid As (i.e. a plural of lipid A) c) Creating a new record called Lipid A (E. coli) which has the structure that is currently on CHEBI:47040.

Would this sort the problem for you? If we did this, are there any current child terms of lipid As (CHEBI:25051) that you might cause you problems?

Cheers, Gareth

alanbridge commented 7 years ago

Sorry to interrupt but I could not help noticing that lipid A (CHEBI:47040) actually has the same connectivity as diphospho hexaacyl lipid A (CHEBI:34724).

The main difference between the two seems to be the orientation of the OH groups on the acyl chains.

CHEBI:34724 maps to KEGG C13908, but that KEGG compound actually has the same InChI key as CHEBI:47040 (OH groups have a specific orientation), so the ChEBI-KEGG mapping is not quite right.

One option could be to merge CHEBI:47040 and CHEBI:34724, or make the former a child of the latter if you want to keep the ambiguity about the OH group orientation (don't know if that is really crucial in lipid A).

alanbridge commented 7 years ago

Forgot to mention, will check this with the Rhea curators too - the corresponding charged species is used in several reactions and the UniProt name is also too generic http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:58712.