search

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
Creative Commons Attribution 4.0 International
43 stars 10 forks source link

60525, correction #1990

Open muthuvenkat opened 14 years ago

muthuvenkat commented 14 years ago

Hi,

I created a structure that did not correspond to the name. Please change the two -OH groups on the phosphate to -O(-)

/Kristian

Reported by: axelsen

muthuvenkat commented 14 years ago

Hi,

The Mo coordination could be as seen in PDBeChem MTQ Please also add x-ref to MTQ from the conjugated_acid.

I can see that Jane Lomax has created compounds without structures for GO (see chebi:60198). Please do something with these compounds so I do not end up with name clashes.

Original comment by: axelsen

muthuvenkat commented 14 years ago

Original comment by: G-Owen

muthuvenkat commented 14 years ago

Hi Kristian,

I have added two negative charges to the structure as requested. However, I am not clear whether CHEBI:60525 represents the same as entity as CHEBI:60102 or CHEBI:60103 - please advise.

Cheers, Gareth

Original comment by: G-Owen

muthuvenkat commented 13 years ago

Hi Steve,

This is a difficult question. As 60103 is depicted now, it is wrong, since MoCo would not be ligated to a free Cys amino acid, but only to a Cys in a protein. Furthermore, the Cys - protein bound or not - is not part of the MoCo, it is only a ligand. I don't like 60102 either since there is a double bond to the S

So I would probably like to see a single bond to an S-R, but I hoped you as chemists could help me find out exactly how this is organised.

/Kristian 60525 is certainly not the same entity as 60103 as this includes a free flying Cys residue (i.e. not part of a protein). It could be considered the same as 60102 but there is the S-ligand in difference. It is difficult from the available structures to see whether this S-ligand is important or not, or whether it is really a difference between different proteins.

That is why I created the structure without the S-ligand, as this can always be used. As stated above I find 60103 wrong as it is depicted currently since MoCo would only be ligated to a Cys in a protein.

/Kristian

Original comment by: axelsen

muthuvenkat commented 13 years ago

Original comment by: axelsen

muthuvenkat commented 13 years ago

Original comment by: mennis