from rdkit.Chem.Scaffolds import MurckoScaffold from rdkit.Chem import AllChem source = 'C(=O)(C)O[C@H]1[C@H]([C@H](n2c3c(c(ncn3)N)nc2)O[C@@H]1CO)O' mol = Chem.MolFromSmiles(source) core = MurckoScaffold.GetScaffoldForMol(mol) print(Chem.MolToSmiles(core)) >>> c1ncc2ncn(C3CCCO3)c2n1