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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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CHEBI:74057 (13E)-16-carboxy-Δ13-17,18,19,20-tetranor-leukotriene E4, needs a review #4191

Open ANiknejad opened 2 years ago

ANiknejad commented 2 years ago

Hello Chebi Team,

This compound was created some times ago from a request available in issue #2766 It is (3E,5Z,7E,9E,11R,12S)-11-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-12-hydroxyhexadeca-3,5,7,9-tetraenedioic acid

A similar compound is available in LipidMaps, https://www.lipidmaps.org/databases/lmsd/LMFA03020051?LMID=LMFA03020051 which is '[(2S)-2-amino...' but this LipidMaps compound is not available into Chebi. I am wondering if one or the other structure may be a mistake, or if both compounds exist?

I do not find any reaction associated with CHEBI:74057 into Rhea, but LMFA03020051 is reported as a xref for a reaction available in the Cricetulus griseus BiGG Models Database, but none Chinese Hamster 'Acyl-coenzyme A thioesterase' enzyme is available as a reviewed entry into UniProt http://bigg.ucsd.edu/universal/metabolites/CE6228

Any help will be greatly appreciated, thank you in advance

Anne

amalik01 commented 2 years ago

Hi Anne,

I think LipidMaps may have got the structure wrong since the the structure of this compound should be based on the structure of leukotriene E4 which has an L-cysteine moiety attached that has R-configuration at the stereo center. See structure of leukotriene E4 (https://commonchemistry.cas.org/detail?cas_rn=75715-89-8&search=75715-89-8). So i'm not sure where they got the S-configuration from.

ANiknejad commented 2 years ago

Hi Adnan,

Many thanks for quick answer, greatly appreciated. I will check with LipidMaps and will let you informed. Anne

ANiknejad commented 2 years ago

@amalik01 Here the very quick answer from LipidMaps, Matthew Conroy ConroyM2@cardiff.ac.uk

Dear Anne, Thanks for your message. A D-cysteine seems unlikely for a naturally occurring molecule, but regrettably (but in common with many other chemical databases) no provenance was recorded at the time this molecule was curated into LIPID MAPS, so I can't tell you anything about it. This is a huge issue I have and I'm working to rectify it. All new LIPID MAPS entries now come with literature references.

It's probable that this is an error, but I can't rule out the possibility that it is some synthetic compound which has been brought into the database. We also have LMFA03020055, which is the L-form of the cysteine, but seems to have ambiguous double-bond geometry at C3-C4.

There is a vicious cycle of (blindly) swapping data between databases so the presence of a compound in several places proves nothing. It is this sort of thing, along with people not being sceptical, which I think will lead to the ultimate downfall of bioinformatics as a field.

I'll do some digging in the literature and see if I can track any literature for either of these compounds.

regards

Matt