data_KPS # _chem_comp.id KPS _chem_comp.name "pseudouridine 5'-phosphate, linear" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H15 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "1-deoxy-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-ribitol" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-08-16 _chem_comp.pdbx_modified_date 2020-06-17 _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 326.197 _chem_comp.one_letter_code ? _chem_comp.three_letter_code KPS _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 4GIL _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 KPS O3T O3T O 0 1 N N N -2.960 -35.832 14.921 -6.208 0.579 -1.469 O3T KPS 1 KPS P P P 0 1 N N N -3.606 -36.370 13.669 -5.354 -0.007 -0.236 P KPS 2 KPS O1P O1P O 0 1 N N N -2.769 -36.218 12.422 -5.742 0.693 1.009 O1P KPS 3 KPS O2P O2P O 0 1 N N N -5.054 -35.985 13.498 -5.649 -1.582 -0.080 O2P KPS 4 KPS "O5'" "O5'" O 0 1 N N N -3.654 -37.959 13.912 -3.785 0.221 -0.514 "O5'" KPS 5 KPS "C5'" "C5'" C 0 1 N N N -4.534 -38.784 13.153 -2.772 -0.097 0.443 "C5'" KPS 6 KPS "C4'" "C4'" C 0 1 N N R -3.974 -40.200 13.098 -1.397 0.241 -0.139 "C4'" KPS 7 KPS "O4'" "O4'" O 0 1 N N N -2.550 -40.151 13.234 -1.299 1.652 -0.339 "O4'" KPS 8 KPS "C3'" "C3'" C 0 1 N N S -4.560 -41.059 14.211 -0.306 -0.213 0.832 "C3'" KPS 9 KPS "O3'" "O3'" O 0 1 N N N -5.641 -40.354 14.832 -0.405 -1.625 1.033 "O3'" KPS 10 KPS "C2'" "C2'" C 0 1 N N S -5.073 -42.388 13.669 1.068 0.125 0.251 "C2'" KPS 11 KPS "O2'" "O2'" O 0 1 N N N -5.440 -42.233 12.293 1.166 1.536 0.050 "O2'" KPS 12 KPS "C1'" "C1'" C 0 1 N N N -4.027 -43.491 13.794 2.159 -0.330 1.222 "C1'" KPS 13 KPS C5 C5 C 0 1 N N N -4.139 -44.462 12.623 3.512 -0.109 0.597 C5 KPS 14 KPS C6 C6 C 0 1 N N N -4.675 -45.734 13.104 4.208 1.019 0.853 C6 KPS 15 KPS N1 N1 N 0 1 N N N -4.015 -46.886 12.955 5.436 1.203 0.277 N1 KPS 16 KPS C2 C2 C 0 1 N N N -2.812 -46.937 12.350 5.955 0.271 -0.542 C2 KPS 17 KPS O2 O2 O 0 1 N N N -2.229 -48.035 12.231 7.048 0.455 -1.043 O2 KPS 18 KPS N3 N3 N 0 1 N N N -2.233 -45.830 11.876 5.283 -0.863 -0.814 N3 KPS 19 KPS C4 C4 C 0 1 N N N -2.815 -44.631 11.979 4.073 -1.085 -0.262 C4 KPS 20 KPS O4 O4 O 0 1 N N N -2.229 -43.629 11.517 3.464 -2.111 -0.507 O4 KPS 21 KPS H1 H1 H 0 1 N N N -2.105 -35.475 14.709 -7.164 0.476 -1.370 H1 KPS 22 KPS H2 H2 H 0 1 N N N -5.203 -35.701 12.604 -5.418 -2.105 -0.861 H2 KPS 23 KPS H3 H3 H 0 1 N N N -4.623 -38.384 12.132 -2.934 0.483 1.351 H3 KPS 24 KPS H4 H4 H 0 1 N N N -5.526 -38.799 13.629 -2.815 -1.161 0.678 H4 KPS 25 KPS H5 H5 H 0 1 N N N -4.243 -40.647 12.130 -1.271 -0.271 -1.093 H5 KPS 26 KPS H6 H6 H 0 1 N N N -2.198 -41.033 13.200 -1.402 2.172 0.469 H6 KPS 27 KPS H7 H7 H 0 1 N N N -3.772 -41.262 14.951 -0.433 0.299 1.786 H7 KPS 28 KPS H8 H8 H 0 1 N N N -6.009 -40.887 15.527 -0.301 -2.145 0.224 H8 KPS 29 KPS H9 H9 H 0 1 N N N -5.957 -42.682 14.254 1.194 -0.387 -0.703 H9 KPS 30 KPS H10 H10 H 0 1 N N N -6.092 -41.546 12.214 1.063 2.056 0.859 H10 KPS 31 KPS H11 H11 H 0 1 N N N -4.187 -44.038 14.735 2.087 0.246 2.145 H11 KPS 32 KPS H12 H12 H 0 1 N N N -3.023 -43.041 13.797 2.029 -1.389 1.444 H12 KPS 33 KPS H14 H14 H 0 1 N N N -5.636 -45.743 13.596 3.798 1.773 1.508 H14 KPS 34 KPS H15 H15 H 0 1 N N N -1.340 -45.900 11.432 5.674 -1.527 -1.403 H15 KPS 35 KPS H13 H13 H 0 1 N N N -4.424 -47.731 13.301 5.936 2.014 0.461 H13 KPS 36 # # 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 KPS O4 C4 DOUB N N 1 KPS N3 C4 SING N N 2 KPS N3 C2 SING N N 3 KPS C4 C5 SING N N 4 KPS O2 C2 DOUB N N 5 KPS "O2'" "C2'" SING N N 6 KPS C2 N1 SING N N 7 KPS O1P P DOUB N N 8 KPS C5 C6 DOUB N N 9 KPS C5 "C1'" SING N N 10 KPS N1 C6 SING N N 11 KPS "C4'" "C5'" SING N N 12 KPS "C4'" "O4'" SING N N 13 KPS "C4'" "C3'" SING N N 14 KPS "C5'" "O5'" SING N N 15 KPS O2P P SING N N 16 KPS "C2'" "C1'" SING N N 17 KPS "C2'" "C3'" SING N N 18 KPS P "O5'" SING N N 19 KPS P O3T SING N N 20 KPS "C3'" "O3'" SING N N 21 KPS O3T H1 SING N N 22 KPS O2P H2 SING N N 23 KPS "C5'" H3 SING N N 24 KPS "C5'" H4 SING N N 25 KPS "C4'" H5 SING N N 26 KPS "O4'" H6 SING N N 27 KPS "C3'" H7 SING N N 28 KPS "O3'" H8 SING N N 29 KPS "C2'" H9 SING N N 30 KPS "O2'" H10 SING N N 31 KPS "C1'" H11 SING N N 32 KPS "C1'" H12 SING N N 33 KPS C6 H14 SING N N 34 KPS N3 H15 SING N N 35 KPS N1 H13 SING N N 36 # # 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 KPS SMILES ACDLabs 12.01 "O=C1C(=CNC(=O)N1)CC(O)C(O)C(O)COP(=O)(O)O" KPS InChI InChI 1.03 "InChI=1S/C9H15N2O9P/c12-5(1-4-2-10-9(16)11-8(4)15)7(14)6(13)3-20-21(17,18)19/h2,5-7,12-14H,1,3H2,(H2,17,18,19)(H2,10,11,15,16)/t5-,6+,7-/m0/s1" KPS InChIKey InChI 1.03 GIMVKTFECLUQAU-XVMARJQXSA-N KPS SMILES_CANONICAL CACTVS 3.370 "O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H](O)CC1=CNC(=O)NC1=O" KPS SMILES CACTVS 3.370 "O[CH](CO[P](O)(O)=O)[CH](O)[CH](O)CC1=CNC(=O)NC1=O" KPS SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=C(C(=O)NC(=O)N1)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O" KPS SMILES "OpenEye OEToolkits" 1.7.6 "C1=C(C(=O)NC(=O)N1)CC(C(C(COP(=O)(O)O)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 KPS "SYSTEMATIC NAME" ACDLabs 12.01 "1-deoxy-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-ribitol" KPS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4S)-5-[2,4-bis(oxidanylidene)-1H-pyrimidin-5-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site KPS "Create component" 2012-08-16 RCSB KPS "Modify name" 2012-09-12 RCSB KPS "Initial release" 2012-10-26 RCSB KPS "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id KPS _pdbx_chem_comp_synonyms.name "1-deoxy-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-ribitol" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##