data_A1DOD # _chem_comp.id A1DOD _chem_comp.name "4-(methylsulfanyl)-1,5-dihydro-2H-cyclopenta[d]pyrimidin-2-one" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C8 H8 N2 O S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2026-07-23 _chem_comp.pdbx_modified_date 2026-07-31 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 180.227 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1DOD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 14VA _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal A1DOD C1 C1 C 0 1 N N N N N N 4.561 62.951 7.306 3.419 0.372 0.002 C1 A1DOD 1 A1DOD S1 S1 S 0 1 N N N N N N 5.866 63.259 8.493 1.969 1.456 -0.002 S1 A1DOD 2 A1DOD C2 C2 C 0 1 N N N N N N 7.192 62.257 7.901 0.685 0.249 -0.002 C2 A1DOD 3 A1DOD N1 N1 N 0 1 N N N N N N 6.878 61.385 6.947 0.983 -1.048 0.001 N1 A1DOD 4 A1DOD C3 C3 C 0 1 N N N N N N 7.848 60.592 6.417 0.025 -1.971 0.001 C3 A1DOD 5 A1DOD O1 O1 O 0 1 N N N N N N 7.566 59.792 5.515 0.336 -3.151 0.004 O1 A1DOD 6 A1DOD N2 N2 N 0 1 N N N N N N 9.150 60.659 6.869 -1.279 -1.636 -0.001 N2 A1DOD 7 A1DOD C4 C4 C 0 1 N N N N N N 9.470 61.546 7.849 -1.650 -0.312 -0.004 C4 A1DOD 8 A1DOD C5 C5 C 0 1 N N N N N N 8.510 62.355 8.371 -0.657 0.646 0.001 C5 A1DOD 9 A1DOD C6 C6 C 0 1 N N N N N N 9.116 63.252 9.422 -1.349 1.985 0.005 C6 A1DOD 10 A1DOD C7 C7 C 0 1 N N N N N N 10.617 62.903 9.411 -2.828 1.668 0.007 C7 A1DOD 11 A1DOD C8 C8 C 0 1 N N N N N N 10.823 61.742 8.429 -2.959 0.347 -0.007 C8 A1DOD 12 A1DOD H1 H1 H 0 1 N N N N N N 3.670 63.534 7.581 3.401 -0.255 0.893 H1 A1DOD 13 A1DOD H2 H2 H 0 1 N N N N N N 4.900 63.250 6.303 3.404 -0.259 -0.887 H2 A1DOD 14 A1DOD H3 H3 H 0 1 N N N N N N 4.312 61.880 7.305 4.325 0.978 0.002 H3 A1DOD 15 A1DOD H4 H4 H 0 1 N N N N N N 9.851 60.061 6.480 -1.957 -2.330 -0.001 H4 A1DOD 16 A1DOD H5 H5 H 0 1 N N N N N N 8.961 64.310 9.166 -1.082 2.546 0.900 H5 A1DOD 17 A1DOD H6 H6 H 0 1 N N N N N N 8.676 63.046 10.409 -1.085 2.550 -0.890 H6 A1DOD 18 A1DOD H7 H7 H 0 1 N N N N N N 11.387 63.389 9.991 -3.633 2.388 0.010 H7 A1DOD 19 A1DOD H10 H8 H 0 1 N N N N N N 11.731 61.199 8.212 -3.905 -0.173 -0.007 H10 A1DOD 20 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A1DOD C1 S1 SING N N 1 A1DOD S1 C2 SING N N 2 A1DOD C2 N1 DOUB N N 3 A1DOD N1 C3 SING N N 4 A1DOD C3 O1 DOUB N N 5 A1DOD C3 N2 SING N N 6 A1DOD N2 C4 SING N N 7 A1DOD C4 C5 DOUB N N 8 A1DOD C5 C6 SING N N 9 A1DOD C6 C7 SING N N 10 A1DOD C7 C8 DOUB N N 11 A1DOD C2 C5 SING N N 12 A1DOD C4 C8 SING N N 13 A1DOD C1 H1 SING N N 14 A1DOD C1 H2 SING N N 15 A1DOD C1 H3 SING N N 16 A1DOD N2 H4 SING N N 17 A1DOD C6 H5 SING N N 18 A1DOD C6 H6 SING N N 19 A1DOD C7 H7 SING N N 20 A1DOD C8 H10 SING N N 21 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor A1DOD SMILES ACDLabs 14.52 "CSC1=NC(=O)NC=2C=CCC=21" A1DOD InChI InChI 1.06 "InChI=1S/C8H8N2OS/c1-12-7-5-3-2-4-6(5)9-8(11)10-7/h2,4H,3H2,1H3,(H,9,10,11)" A1DOD InChIKey InChI 1.06 KDOKCBRZLDKPAE-UHFFFAOYSA-N A1DOD SMILES_CANONICAL CACTVS 3.385 "CSC1=NC(=O)NC2=C1CC=C2" A1DOD SMILES CACTVS 3.385 "CSC1=NC(=O)NC2=C1CC=C2" A1DOD SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "CSC1=NC(=O)NC2=C1CC=C2" A1DOD SMILES "OpenEye OEToolkits" 3.1.0.0 "CSC1=NC(=O)NC2=C1CC=C2" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier A1DOD "SYSTEMATIC NAME" ACDLabs 14.52 "4-(methylsulfanyl)-1,5-dihydro-2H-cyclopenta[d]pyrimidin-2-one" A1DOD "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "4-methylsulfanyl-1,5-dihydrocyclopenta[d]pyrimidin-2-one" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1DOD "Create component" 2026-07-23 RCSB A1DOD "Initial release" 2026-08-05 RCSB #