data_Q87 # _chem_comp.id Q87 _chem_comp.name "1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H18 N4 O7" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-10-02 _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 330.294 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Q87 _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 6PUC _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 Q87 C4 C1 C 0 1 N N N 44.811 72.565 226.840 1.246 0.919 0.083 C4 Q87 1 Q87 C5 C2 C 0 1 N N N 43.214 71.420 228.354 -1.199 0.828 0.013 C5 Q87 2 Q87 C6 C3 C 0 1 N N S 41.722 71.405 228.042 -2.307 -0.217 0.161 C6 Q87 3 Q87 C8 C4 C 0 1 N N R 39.737 72.895 227.499 -4.778 -0.587 0.140 C8 Q87 4 Q87 N1 N1 N 0 1 N N N 44.154 71.421 227.231 0.105 0.182 0.175 N1 Q87 5 Q87 N3 N2 N 0 1 N N N 46.064 74.907 226.166 3.530 2.480 -0.116 N3 Q87 6 Q87 O6 O1 O 0 1 N N N 47.622 73.862 224.906 4.814 0.690 0.240 O6 Q87 7 Q87 C2 C5 C 0 1 N N N 47.388 71.070 224.949 3.455 -1.730 -0.237 C2 Q87 8 Q87 O2 O2 O 0 1 N N N 41.813 73.775 228.409 -3.830 1.466 0.992 O2 Q87 9 Q87 N N3 N 0 1 N N N 46.311 71.264 225.624 2.616 -1.008 0.464 N Q87 10 Q87 C C6 C 0 1 N N N 47.062 68.625 225.439 4.618 -3.919 -0.725 C Q87 11 Q87 C1 C7 C 0 1 N N N 47.799 69.694 224.680 3.653 -3.089 0.081 C1 Q87 12 Q87 C10 C8 C 0 1 N N N 44.966 74.970 226.985 2.301 3.004 -0.253 C10 Q87 13 Q87 C11 C9 C 0 1 N N N 46.607 73.771 225.597 3.698 1.163 0.120 C11 Q87 14 Q87 C3 C10 C 0 1 N N N 45.902 72.553 225.951 2.506 0.309 0.231 C3 Q87 15 Q87 C7 C11 C 0 1 N N S 41.262 72.775 227.545 -3.670 0.458 -0.008 C7 Q87 16 Q87 C9 C12 C 0 1 N N N 39.125 72.686 228.875 -6.141 0.087 -0.029 C9 Q87 17 Q87 N2 N4 N 0 1 N N N 44.381 73.769 227.310 1.187 2.262 -0.159 N2 Q87 18 Q87 O1 O3 O 0 1 N N N 41.453 70.354 227.111 -2.148 -1.225 -0.839 O1 Q87 19 Q87 O3 O4 O 0 1 N N N 39.413 74.206 227.054 -4.619 -1.595 -0.860 O3 Q87 20 Q87 O4 O5 O 0 1 N N N 37.734 72.970 228.856 -7.178 -0.863 0.224 O4 Q87 21 Q87 O5 O6 O 0 1 N N N 44.520 76.041 227.384 2.194 4.196 -0.465 O5 Q87 22 Q87 H1 H1 H 0 1 N N N 43.430 70.528 228.960 -1.259 1.283 -0.975 H1 Q87 23 Q87 H2 H2 H 0 1 N N N 43.414 72.324 228.948 -1.321 1.597 0.776 H2 Q87 24 Q87 H3 H3 H 0 1 N N N 41.187 71.195 228.980 -2.248 -0.673 1.149 H3 Q87 25 Q87 H4 H4 H 0 1 N N N 39.337 72.140 226.806 -4.719 -1.043 1.128 H4 Q87 26 Q87 H5 H5 H 0 1 N N N 43.640 71.105 226.433 0.157 -0.771 0.347 H5 Q87 27 Q87 H6 H6 H 0 1 N N N 46.519 75.773 225.959 4.307 3.056 -0.192 H6 Q87 28 Q87 H7 H7 H 0 1 N N N 47.974 71.903 224.590 3.995 -1.283 -1.059 H7 Q87 29 Q87 H8 H8 H 0 1 N N N 42.759 73.690 228.429 -3.787 1.131 1.898 H8 Q87 30 Q87 H9 H9 H 0 1 N N N 47.575 67.661 225.308 5.615 -3.485 -0.657 H9 Q87 31 Q87 H10 H10 H 0 1 N N N 47.038 68.885 226.508 4.637 -4.936 -0.334 H10 Q87 32 Q87 H11 H11 H 0 1 N N N 46.033 68.547 225.057 4.299 -3.937 -1.767 H11 Q87 33 Q87 H15 H15 H 0 1 N N N 41.648 72.918 226.525 -3.730 0.913 -0.997 H15 Q87 34 Q87 H16 H16 H 0 1 N N N 39.276 71.640 229.182 -6.227 0.915 0.675 H16 Q87 35 Q87 H17 H17 H 0 1 N N N 39.620 73.354 229.595 -6.236 0.466 -1.047 H17 Q87 36 Q87 H18 H18 H 0 1 N N N 41.758 69.528 227.468 -2.190 -0.891 -1.745 H18 Q87 37 Q87 H19 H19 H 0 1 N N N 38.469 74.304 227.017 -4.661 -1.261 -1.767 H19 Q87 38 Q87 H20 H20 H 0 1 N N N 37.371 72.834 229.723 -8.071 -0.504 0.134 H20 Q87 39 Q87 O7 O7 O 0 1 N N N 48.936 69.142 224.021 3.045 -3.591 1.006 O7 Q87 40 Q87 H12 H12 H 0 1 N N N 43.594 73.780 227.927 0.322 2.688 -0.266 H12 Q87 41 # # 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 Q87 C1 C2 SING N N 1 Q87 C1 C SING N N 2 Q87 O6 C11 DOUB N N 3 Q87 C2 N DOUB N N 4 Q87 C11 C3 SING N N 5 Q87 C11 N3 SING N N 6 Q87 N C3 SING N N 7 Q87 C3 C4 DOUB N N 8 Q87 N3 C10 SING N N 9 Q87 C4 N1 SING N N 10 Q87 C4 N2 SING N N 11 Q87 C10 N2 SING N N 12 Q87 C10 O5 DOUB N N 13 Q87 O3 C8 SING N N 14 Q87 O1 C6 SING N N 15 Q87 N1 C5 SING N N 16 Q87 C8 C7 SING N N 17 Q87 C8 C9 SING N N 18 Q87 C7 C6 SING N N 19 Q87 C7 O2 SING N N 20 Q87 C6 C5 SING N N 21 Q87 O4 C9 SING N N 22 Q87 C5 H1 SING N N 23 Q87 C5 H2 SING N N 24 Q87 C6 H3 SING N N 25 Q87 C8 H4 SING N N 26 Q87 N1 H5 SING N N 27 Q87 N3 H6 SING N N 28 Q87 C2 H7 SING N N 29 Q87 O2 H8 SING N N 30 Q87 C H9 SING N N 31 Q87 C H10 SING N N 32 Q87 C H11 SING N N 33 Q87 C7 H15 SING N N 34 Q87 C9 H16 SING N N 35 Q87 C9 H17 SING N N 36 Q87 O1 H18 SING N N 37 Q87 O3 H19 SING N N 38 Q87 O4 H20 SING N N 39 Q87 C1 O7 DOUB N N 40 Q87 N2 H12 SING N N 41 # # 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 Q87 SMILES ACDLabs 12.01 "C=1(NCC(C(C(CO)O)O)O)NC(NC(=O)C=1N=[C@H]C(C)=O)=O" Q87 InChI InChI 1.03 "InChI=1S/C12H18N4O7/c1-5(18)2-13-8-10(15-12(23)16-11(8)22)14-3-6(19)9(21)7(20)4-17/h2,6-7,9,17,19-21H,3-4H2,1H3,(H3,14,15,16,22,23)/b13-2+/t6-,7+,9-/m0/s1" Q87 InChIKey InChI 1.03 LXKLTDXEFFOBPT-CEKOQDAHSA-N Q87 SMILES_CANONICAL CACTVS 3.385 "CC(=O)C=NC1=C(NC[C@H](O)[C@H](O)[C@H](O)CO)NC(=O)NC1=O" Q87 SMILES CACTVS 3.385 "CC(=O)C=NC1=C(NC[CH](O)[CH](O)[CH](O)CO)NC(=O)NC1=O" Q87 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=O)/C=N/C1=C(NC(=O)NC1=O)NC[C@@H]([C@@H]([C@@H](CO)O)O)O" Q87 SMILES "OpenEye OEToolkits" 2.0.7 "CC(=O)C=NC1=C(NC(=O)NC1=O)NCC(C(C(CO)O)O)O" # # 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 Q87 "SYSTEMATIC NAME" ACDLabs 12.01 "1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol" Q87 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "5-[(~{E})-2-oxidanylidenepropylideneamino]-6-[[(2~{S},3~{S},4~{R})-2,3,4,5-tetrakis(oxidanyl)pentyl]amino]-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 Q87 "Create component" 2019-10-02 RCSB Q87 "Initial release" 2020-02-19 RCSB ##