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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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Please, update structures #4386

Closed amorgat closed 1 year ago

amorgat commented 1 year ago

Dear Adnan, We have some trouble in the processing of the compounds (see below) that are used in Rhea. Would you mind replacing their structures with the attached Molfiles that I redrew from scratch? PS: Kristian and I updated the structure of some of our submissions and it fixed the processing issue. Thank you for your support, Anne

17791 obtusifoliol 30834 aldosterone hemiacetal 30997 levoglucosan 42870 N-acetyl-D-glucosamino-1,5-lactone 50068 stemod-13(17)-ene 58690 1,6-anhydro-N-acetyl-beta-muramate 131146 dihydroouabain 131711 (S)-demethyl-4-deoxygadusol(1-) 132139 (R)-demethyl-4-deoxygadusol(1-) 144894 3-dehydrolevoglucosan 173121 (1S,6S,7R)-sesquipiperitol 183368 7beta-hydroxydehydroepiandrosterone

chebi_58690_updated.mol.txt chebi_50068_updated.mol.txt chebi_42870_updated.mol.txt chebi_30997_updated.mol.txt chebi_30834_updated.mol.txt chebi_183368_updated.mol.txt chebi_17791_updated.mol.txt chebi_173121_updated.mol.txt chebi_144894_updated.mol.txt chebi_132139_updated.mol.txt chebi_131711_updated.mol.txt chebi_131146_updated.mol.txt

amalik01 commented 1 year ago

@amorgat Do you know what exactly is wrong with the current mol files?

amalik01 commented 1 year ago

@amorgat Can you please check whether the mol files are fine now or still causing issues? I haven't yet updated the mol files but left a space at the top of the file to figure out whether this is the issue.

amorgat commented 1 year ago

CHEBI:17791 If I load the old Molfile in MarvinSketch and export it as SMILES, the stereoX is missing [H]C1(CCC2(C)C3=C(CCC12C)C1(C)CCC(O)C(C)C1([H])CC3)C(C)CCC(=C)C(C)C

With your recently updated version, the stereoX is as expected [H][C@@]1(CC[C@@]2(C)C3=C(CC[C@]12C)[C@@]1(C)CCC@HC@@H[C@]1([H])CC3)C@HCCC(=C)C(C)C

I can see in the chebi curator tool (structure history) that the bond block is different: 7 columns in the old Molfile, 6 in the new one. Can you confirm that you made other changes than just adding a left space at the top for CHEBI:17791?

SIB local copy: I have to wait the synchro to get the result of the computation with the new structure of CHEBI:17791

amalik01 commented 1 year ago

The mol files for all of the above structures have now been updated.