Prediction of protonation states of ChEMBL33 compounds with MW <= 500

These are structures retrieved from ChEMBL33, which were filtered by MW <= 500, for each compounds the stable tautomer was generated by chemaxon and all stereoisomers were enumerated by RDKit. chembl_stereo.smi is a tab-separated file with SMILES for all enumerated stereoisomers, which can be used to predict protonation states by approaches using 3D representation for which stereoinformation should be important. Example of the content start_smi id base_id stereo_idO=c1oc(Nc2ccc(I)cc2)nc2ccccc12 CHEMBL10000_1 CHEMBL10000 1N[C@@H](Cc1c[nH]cn1)C(=O)N[C@@H](Cc1c[nH]cn1)C(=O)N[C@@H](Cc1c[nH]cn1)C(=O)O CHEMBL100001_1 CHEMBL100001 1CCC[C@@H]1C(C(=O)OC)=C(C)NC(C)=C1C(=O)OCC CHEMBL100003_1 CHEMBL100003 1CCC[C@H]1C(C(=O)OC)=C(C)NC(C)=C1C(=O)OCC CHEMBL100003_2 CHEMBL100003 2 chembl_nostereo.smi is a tab-separated file with unsteric SMILES for the same ChEMBL compounds as above and predicted protonation states at pH 7.4 by Chemaxon, MolGpKa, MolGpKa and pkasolver both integrated in EasyDock (there some fixes were implemented), pka-predictor. chembl_nostereo_changed_only.smi is a subset of chembl_nostereo.smi with removed structures which were not changed in all programs. This may facilitate further tests and the analysis. All SMILES were generated using RDKit 2025.03.5.