Dear all,
I encountered a problem when reading the molecule “Oxaliplatin”. In DrugBank, the SMILES of Oxaliplatin is `[H][N]1([H])[C@@H]2CCCC[C@H]2[N]([H])([H])[Pt]11OC(=O)C(=O)O1`. If you use Chem.MolFromSmiles without denying sanitisation, it will return an error, "Explicit valence for atom # 0 N, 4, is greater than permitted”. In this molecule, the nitrogens have four bonds, one of which is coordination bond. It seems that SMILES cannot present this bond type. My question is how to read it? Sanitisation is necessary to e.g. calculate fingerprint so skipping sanitisation is not a good idea. One alternative is to use ionisation. For example, the SMILES of Oxaliplatin in PubChem is `C1CC[C@H]([C@@H](C1)[NH-])[NH-].C(=O)(C(=O)[O-])[O-].[Pt+4]`. It transfers the covalent bonds into ionic bonds, which I think is not good enough, but it’s OK. If this is the only solution, my question is how to transfer the “incorrect” SMILES in DrugBank into the “correct” one in PubChem within RDKit. PS, I though it should be a common issue but I could not find anything similar in GitHub Issue and Mailing list history. (Maybe it is because we are always discarding organometallic compounds ?) Best regards, Hongbin Yang 杨弘宾, Ph.D. Research: Toxicophore and Chemoinformatics Pharmaceutical Science, School of Pharmacy East China University of Science and Technology
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