data_OYD # _chem_comp.id OYD _chem_comp.name "6-[(5-hydroxypentyl)amino]-5-[(E)-propylideneamino]pyrimidine-2,4(1H,3H)-dione" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H20 N4 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-07-18 _chem_comp.pdbx_modified_date 2020-02-14 _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 268.312 _chem_comp.one_letter_code ? _chem_comp.three_letter_code OYD _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 6PUD _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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.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 OYD C4 C1 C 0 1 N N N 46.662 72.852 225.977 0.790 0.639 -0.082 C4 OYD 1 OYD C5 C2 C 0 1 N N N 44.899 71.913 227.294 -1.663 0.594 -0.012 C5 OYD 2 OYD C6 C3 C 0 1 N N N 43.516 71.804 226.707 -2.790 -0.438 -0.087 C6 OYD 3 OYD C8 C4 C 0 1 N N N 41.071 71.831 227.507 -5.268 -0.759 -0.046 C8 OYD 4 OYD N1 N1 N 0 1 N N N 45.996 71.720 226.353 -0.370 -0.086 -0.124 N1 OYD 5 OYD N3 N2 N 0 1 N N N 48.029 75.130 225.351 3.095 2.126 0.006 N3 OYD 6 OYD C2 C5 C 0 1 N N N 49.261 71.279 224.210 2.902 -2.046 0.391 C2 OYD 7 OYD O2 O1 O 0 1 N N N 46.426 76.338 226.376 1.831 3.924 0.241 O2 OYD 8 OYD N N3 N 0 1 N N N 48.177 71.492 224.873 2.098 -1.356 -0.347 N OYD 9 OYD C C6 C 0 1 N N N 48.903 68.869 224.800 4.325 -4.038 -0.003 C OYD 10 OYD C1 C7 C 0 1 N N N 49.550 69.879 223.893 2.906 -3.550 0.298 C1 OYD 11 OYD C10 C8 C 0 1 N N N 46.870 75.250 226.064 1.892 2.717 0.105 C10 OYD 12 OYD C11 C9 C 0 1 N N N 48.577 73.964 224.866 3.199 0.791 -0.146 C11 OYD 13 OYD C3 C10 C 0 1 N N N 47.819 72.792 225.198 2.023 0.003 -0.194 C3 OYD 14 OYD C7 C11 C 0 1 N N N 42.531 72.052 227.870 -4.141 0.273 0.030 C7 OYD 15 OYD C9 C12 C 0 1 N N N 40.126 72.430 228.550 -6.618 -0.049 0.072 C9 OYD 16 OYD N2 N4 N 0 1 N N N 46.222 74.080 226.376 0.753 2.003 0.064 N2 OYD 17 OYD O1 O2 O 0 1 N N N 40.222 73.835 228.408 -7.671 -1.013 0.001 O1 OYD 18 OYD O3 O3 O 0 1 N N N 49.618 74.001 224.226 4.295 0.267 -0.240 O3 OYD 19 OYD H1 H1 H 0 1 N N N 44.993 71.154 228.084 -1.770 1.309 -0.828 H1 OYD 20 OYD H2 H2 H 0 1 N N N 45.002 72.916 227.734 -1.716 1.120 0.941 H2 OYD 21 OYD H3 H3 H 0 1 N N N 43.375 72.560 225.921 -2.738 -0.964 -1.040 H3 OYD 22 OYD H4 H4 H 0 1 N N N 43.360 70.801 226.283 -2.684 -1.152 0.729 H4 OYD 23 OYD H5 H5 H 0 1 N N N 40.871 72.303 226.534 -5.215 -1.285 -0.999 H5 OYD 24 OYD H6 H6 H 0 1 N N N 40.882 70.750 227.436 -5.161 -1.474 0.770 H6 OYD 25 OYD H7 H7 H 0 1 N N N 45.622 71.296 225.528 -0.337 -1.049 -0.228 H7 OYD 26 OYD H8 H8 H 0 1 N N N 48.530 75.975 225.162 3.899 2.668 0.039 H8 OYD 27 OYD H9 H9 H 0 1 N N N 49.916 72.083 223.907 3.570 -1.545 1.075 H9 OYD 28 OYD H10 H10 H 0 1 N N N 49.182 67.855 224.478 4.328 -5.126 -0.071 H10 OYD 29 OYD H11 H11 H 0 1 N N N 49.244 69.033 225.833 4.661 -3.615 -0.949 H11 OYD 30 OYD H12 H12 H 0 1 N N N 47.810 68.981 224.753 4.995 -3.721 0.796 H12 OYD 31 OYD H13 H13 H 0 1 N N N 49.205 69.685 222.867 2.570 -3.974 1.244 H13 OYD 32 OYD H14 H14 H 0 1 N N N 50.639 69.736 223.947 2.236 -3.867 -0.501 H14 OYD 33 OYD H16 H16 H 0 1 N N N 42.789 71.369 228.693 -4.193 0.799 0.983 H16 OYD 34 OYD H17 H17 H 0 1 N N N 42.649 73.093 228.207 -4.247 0.987 -0.786 H17 OYD 35 OYD H18 H18 H 0 1 N N N 39.094 72.098 228.365 -6.670 0.477 1.025 H18 OYD 36 OYD H19 H19 H 0 1 N N N 40.433 72.127 229.562 -6.725 0.666 -0.744 H19 OYD 37 OYD H20 H20 H 0 1 N N N 39.650 74.257 229.038 -8.557 -0.633 0.069 H20 OYD 38 OYD H15 H15 H 0 1 N N N 45.386 74.131 226.923 -0.102 2.455 0.138 H15 OYD 39 # # 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 OYD C1 C2 SING N N 1 OYD C1 C SING N N 2 OYD C2 N DOUB N N 3 OYD O3 C11 DOUB N N 4 OYD C11 C3 SING N N 5 OYD C11 N3 SING N N 6 OYD N C3 SING N N 7 OYD C3 C4 DOUB N N 8 OYD N3 C10 SING N N 9 OYD C4 N1 SING N N 10 OYD C4 N2 SING N N 11 OYD C10 N2 SING N N 12 OYD C10 O2 DOUB N N 13 OYD N1 C5 SING N N 14 OYD C6 C5 SING N N 15 OYD C6 C7 SING N N 16 OYD C8 C7 SING N N 17 OYD C8 C9 SING N N 18 OYD O1 C9 SING N N 19 OYD C5 H1 SING N N 20 OYD C5 H2 SING N N 21 OYD C6 H3 SING N N 22 OYD C6 H4 SING N N 23 OYD C8 H5 SING N N 24 OYD C8 H6 SING N N 25 OYD N1 H7 SING N N 26 OYD N3 H8 SING N N 27 OYD C2 H9 SING N N 28 OYD C H10 SING N N 29 OYD C H11 SING N N 30 OYD C H12 SING N N 31 OYD C1 H13 SING N N 32 OYD C1 H14 SING N N 33 OYD C7 H16 SING N N 34 OYD C7 H17 SING N N 35 OYD C9 H18 SING N N 36 OYD C9 H19 SING N N 37 OYD O1 H20 SING N N 38 OYD N2 H15 SING N N 39 # # 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 OYD SMILES ACDLabs 12.01 "C=1(NCCCCCO)NC(NC(C=1N=[C@H]CC)=O)=O" OYD InChI InChI 1.03 "InChI=1S/C12H20N4O3/c1-2-6-13-9-10(14-7-4-3-5-8-17)15-12(19)16-11(9)18/h6,17H,2-5,7-8H2,1H3,(H3,14,15,16,18,19)/b13-6+" OYD InChIKey InChI 1.03 ZKFUQHLXTDAXLG-AWNIVKPZSA-N OYD SMILES_CANONICAL CACTVS 3.385 "CCC=NC1=C(NCCCCCO)NC(=O)NC1=O" OYD SMILES CACTVS 3.385 "CCC=NC1=C(NCCCCCO)NC(=O)NC1=O" OYD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC/C=N/C1=C(NC(=O)NC1=O)NCCCCCO" OYD SMILES "OpenEye OEToolkits" 2.0.7 "CCC=NC1=C(NC(=O)NC1=O)NCCCCCO" # # 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 OYD "SYSTEMATIC NAME" ACDLabs 12.01 "6-[(5-hydroxypentyl)amino]-5-[(E)-propylideneamino]pyrimidine-2,4(1H,3H)-dione" OYD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "6-(5-oxidanylpentylamino)-5-[(~{E})-propylideneamino]-1~{H}-pyrimidine-2,4-dione" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site OYD "Create component" 2019-07-18 RCSB OYD "Other modification" 2019-09-30 RCSB OYD "Initial release" 2020-02-19 RCSB ##