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mSorok / NaturalProductsOnline

Website code for COCONUT
https://coconut.naturalproducts.net/
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CNP0000001 / Picrotoxinin smiles is incorrect : pentavalent carbon results #104

Open WCCS-DRC opened 1 year ago

WCCS-DRC commented 1 year ago

Picrotoxinini smiles generates a strcuture iwth pentavalent carbon due to incorrect linkage in SMILES.

As coded: CC(=C)C1CC2C(=O)OC1[CH]34(C2(CC5C3(O5)C(=O)OC4)O)C or CC(=C)[C@H]1C[C@H]2C(=O)O[C@@H]1[CH]34([C@]2(C[C@@H]5[C@]3(O5)C(=O)OC4)O)C

Should be: OC4(CC1OC12C34C)C(C5C(C)=C)C(OC5C3OC2=O)=O or [H][C@@]12OC(=O)C@([C@@H]1C(C)=C)[C@]3(O)C[C@H]4O[C@]45C(=O)O[C@@]2([H])[C@]35C or equivalent without the pentavalent carbon

Inchi and Inchikey will need updating as well I believe.

sthinius87 commented 9 months ago

I obeserved the same issue. This should be updated. There is a carbon with a valence of six.

steinbeck commented 9 months ago

Thanks for the report. We are aware of this and other similar issues and work diligently to fix the problem. Since this is a systemic issue of the first version of the COCONUT database, we are systematically re-visiting the whole dataset. A fully re-curated version of COCONUT will be released soon.