data_YPG # _chem_comp.id YPG _chem_comp.name ;[3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-y l]-3-oxidanylidene-propyl]phosphonic acid ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H22 N6 O10 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "[3R,4R]-4-guanin-9-yl-3-((S)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-01-12 _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 496.306 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YPG _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 5HHU _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 YPG C4 C1 C 0 1 Y N N 31.648 7.033 23.560 2.807 -1.743 0.134 C4 YPG 1 YPG C5 C2 C 0 1 Y N N 32.177 5.765 23.461 3.700 -2.343 -0.761 C5 YPG 2 YPG C6 C3 C 0 1 N N N 33.374 5.530 24.135 5.021 -2.603 -0.326 C6 YPG 3 YPG C8 C4 C 0 1 Y N N 30.360 5.861 22.342 1.810 -2.115 -1.796 C8 YPG 4 YPG N1 N1 N 0 1 N N N 33.909 6.536 24.811 5.361 -2.260 0.936 N1 YPG 5 YPG N2 N2 N 0 1 N N N 33.954 8.835 25.618 4.819 -1.341 3.038 N2 YPG 6 YPG N3 N3 N 0 1 N N N 32.246 7.988 24.254 3.215 -1.431 1.370 N3 YPG 7 YPG OAI O1 O 0 1 N N N 25.483 6.622 17.744 3.684 4.492 0.598 OAI YPG 8 YPG PBF P1 P 0 1 N N N 26.846 6.214 18.228 2.992 3.203 -0.074 PBF YPG 9 YPG OAJ O2 O 0 1 N N N 27.635 5.749 17.026 3.828 2.723 -1.197 OAJ YPG 10 YPG OAE O3 O 0 1 N N N 26.731 5.123 19.265 2.848 2.036 1.026 OAE YPG 11 YPG CAZ C5 C 0 1 N N S 27.616 7.681 19.061 1.340 3.657 -0.698 CAZ YPG 12 YPG OAF O4 O 0 1 N N N 27.686 8.789 18.205 0.532 4.121 0.387 OAF YPG 13 YPG CAN C6 C 0 1 N N N 28.998 7.260 19.524 0.682 2.433 -1.336 CAN YPG 14 YPG OAT O5 O 0 1 N N N 29.427 8.188 20.463 0.554 1.397 -0.360 OAT YPG 15 YPG CBA C7 C 0 1 N N R 28.667 8.229 21.699 -0.052 0.202 -0.857 CBA YPG 16 YPG CAO C8 C 0 1 N N N 28.188 9.452 21.878 -1.580 0.236 -0.645 CAO YPG 17 YPG NBC N4 N 0 1 N N N 28.589 9.936 23.358 -1.997 -1.116 -0.245 NBC YPG 18 YPG CAU C9 C 0 1 N N N 28.367 11.277 23.876 -3.255 -1.495 0.052 CAU YPG 19 YPG OAB O6 O 0 1 N N N 28.693 11.552 24.985 -3.484 -2.642 0.370 OAB YPG 20 YPG CAL C10 C 0 1 N N N 27.697 12.326 22.991 -4.379 -0.492 -0.012 CAL YPG 21 YPG CAM C11 C 0 1 N N N 27.699 13.698 23.654 -5.694 -1.175 0.368 CAM YPG 22 YPG PBE P2 P 0 1 N N N 29.424 14.381 23.655 -7.053 0.037 0.291 PBE YPG 23 YPG OAG O7 O 0 1 N N N 29.342 15.828 24.066 -8.413 -0.646 0.817 OAG YPG 24 YPG OAH O8 O 0 1 N N N 29.959 14.292 22.244 -6.724 1.202 1.144 OAH YPG 25 YPG OAD O9 O 0 1 N N N 30.304 13.583 24.591 -7.251 0.525 -1.230 OAD YPG 26 YPG CAP C12 C 0 1 N N N 29.135 8.897 23.974 -0.809 -1.989 -0.224 CAP YPG 27 YPG CBB C13 C 0 1 N N R 29.792 8.238 22.756 0.387 -1.026 -0.017 CBB YPG 28 YPG N9 N5 N 0 1 Y N N 30.521 7.060 22.884 1.625 -1.607 -0.543 N9 YPG 29 YPG C2 C14 C 0 1 N N N 33.359 7.744 24.873 4.445 -1.679 1.761 C2 YPG 30 YPG O6 O10 O 0 1 N N N 34.002 4.285 24.107 5.832 -3.125 -1.072 O6 YPG 31 YPG N7 N6 N 0 1 Y N N 31.356 5.047 22.692 3.031 -2.546 -1.921 N7 YPG 32 YPG H1 H1 H 0 1 N N N 29.535 5.582 21.704 1.056 -2.152 -2.568 H1 YPG 33 YPG H2 H2 H 0 1 N N N 34.768 6.379 25.298 6.261 -2.429 1.256 H2 YPG 34 YPG H3 H3 H 0 1 N N N 33.506 9.729 25.639 5.723 -1.518 3.342 H3 YPG 35 YPG H4 H4 H 0 1 N N N 34.812 8.694 26.111 4.178 -0.927 3.637 H4 YPG 36 YPG H5 H5 H 0 1 N N N 25.429 6.496 16.804 4.568 4.324 0.952 H5 YPG 37 YPG H6 H6 H 0 1 N N N 27.182 4.345 18.958 2.312 2.282 1.792 H6 YPG 38 YPG H7 H7 H 0 1 N N N 26.985 7.895 19.936 1.437 4.448 -1.442 H7 YPG 39 YPG H8 H8 H 0 1 N N N 28.084 9.519 18.664 0.403 3.468 1.088 H8 YPG 40 YPG H9 H9 H 0 1 N N N 28.953 6.260 19.979 -0.306 2.704 -1.709 H9 YPG 41 YPG H10 H10 H 0 1 N N N 29.691 7.243 18.670 1.297 2.079 -2.163 H10 YPG 42 YPG H11 H11 H 0 1 N N N 27.963 7.394 21.829 0.188 0.058 -1.910 H11 YPG 43 YPG H12 H12 H 0 1 N N N 28.622 10.135 21.132 -1.830 0.949 0.141 H12 YPG 44 YPG H13 H13 H 0 1 N N N 27.093 9.442 21.773 -2.077 0.518 -1.574 H13 YPG 45 YPG H14 H14 H 0 1 N N N 26.657 12.022 22.801 -4.178 0.323 0.683 H14 YPG 46 YPG H15 H15 H 0 1 N N N 28.241 12.389 22.037 -4.455 -0.096 -1.025 H15 YPG 47 YPG H16 H16 H 0 1 N N N 27.036 14.376 23.096 -5.894 -1.990 -0.327 H16 YPG 48 YPG H17 H17 H 0 1 N N N 27.341 13.605 24.690 -5.618 -1.571 1.381 H17 YPG 49 YPG H18 H18 H 0 1 N N N 29.643 16.378 23.352 -9.179 -0.057 0.804 H18 YPG 50 YPG H19 H19 H 0 1 N N N 31.014 13.188 24.099 -7.469 -0.187 -1.847 H19 YPG 51 YPG H20 H20 H 0 1 N N N 28.380 8.247 24.441 -0.873 -2.697 0.602 H20 YPG 52 YPG H21 H21 H 0 1 N N N 29.874 9.203 24.730 -0.711 -2.520 -1.171 H21 YPG 53 YPG H22 H22 H 0 1 N N N 30.503 8.993 22.388 0.498 -0.761 1.035 H22 YPG 54 # # 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 YPG OAJ PBF DOUB N N 1 YPG OAI PBF SING N N 2 YPG OAF CAZ SING N N 3 YPG PBF CAZ SING N N 4 YPG PBF OAE SING N N 5 YPG CAZ CAN SING N N 6 YPG CAN OAT SING N N 7 YPG OAT CBA SING N N 8 YPG CBA CAO SING N N 9 YPG CBA CBB SING N N 10 YPG CAO NBC SING N N 11 YPG OAH PBE DOUB N N 12 YPG C8 N7 DOUB Y N 13 YPG C8 N9 SING Y N 14 YPG N7 C5 SING Y N 15 YPG CBB N9 SING N N 16 YPG CBB CAP SING N N 17 YPG N9 C4 SING Y N 18 YPG CAL CAM SING N N 19 YPG CAL CAU SING N N 20 YPG NBC CAU SING N N 21 YPG NBC CAP SING N N 22 YPG C5 C4 DOUB Y N 23 YPG C5 C6 SING N N 24 YPG C4 N3 SING N N 25 YPG CAM PBE SING N N 26 YPG PBE OAG SING N N 27 YPG PBE OAD SING N N 28 YPG CAU OAB DOUB N N 29 YPG O6 C6 DOUB N N 30 YPG C6 N1 SING N N 31 YPG N3 C2 DOUB N N 32 YPG N1 C2 SING N N 33 YPG C2 N2 SING N N 34 YPG C8 H1 SING N N 35 YPG N1 H2 SING N N 36 YPG N2 H3 SING N N 37 YPG N2 H4 SING N N 38 YPG OAI H5 SING N N 39 YPG OAE H6 SING N N 40 YPG CAZ H7 SING N N 41 YPG OAF H8 SING N N 42 YPG CAN H9 SING N N 43 YPG CAN H10 SING N N 44 YPG CBA H11 SING N N 45 YPG CAO H12 SING N N 46 YPG CAO H13 SING N N 47 YPG CAL H14 SING N N 48 YPG CAL H15 SING N N 49 YPG CAM H16 SING N N 50 YPG CAM H17 SING N N 51 YPG OAG H18 SING N N 52 YPG OAD H19 SING N N 53 YPG CAP H20 SING N N 54 YPG CAP H21 SING N N 55 YPG CBB H22 SING N N 56 # # 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 YPG InChI InChI 1.03 "InChI=1S/C14H22N6O10P2/c15-14-17-12-11(13(23)18-14)16-6-20(12)7-3-19(9(21)1-2-31(24,25)26)4-8(7)30-5-10(22)32(27,28)29/h6-8,10,22H,1-5H2,(H2,24,25,26)(H2,27,28,29)(H3,15,17,18,23)/t7-,8-,10+/m1/s1" YPG InChIKey InChI 1.03 RBYFDIJTTUISNF-MRTMQBJTSA-N YPG SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3CN(C[C@H]3OC[C@@H](O)[P](O)(O)=O)C(=O)CC[P](O)(O)=O" YPG SMILES CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3CN(C[CH]3OC[CH](O)[P](O)(O)=O)C(=O)CC[P](O)(O)=O" YPG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "c1nc2c(n1[C@@H]3CN(C[C@H]3OC[C@@H](O)P(=O)(O)O)C(=O)CCP(=O)(O)O)N=C(NC2=O)N" YPG SMILES "OpenEye OEToolkits" 2.0.4 "c1nc2c(n1C3CN(CC3OCC(O)P(=O)(O)O)C(=O)CCP(=O)(O)O)N=C(NC2=O)N" # _pdbx_chem_comp_identifier.comp_id YPG _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.4 _pdbx_chem_comp_identifier.identifier "[3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-yl]-3-oxidanylidene-propyl]phosphonic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YPG "Create component" 2016-01-12 RCSB YPG "Initial release" 2017-01-18 RCSB YPG "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id YPG _pdbx_chem_comp_synonyms.name "[3R,4R]-4-guanin-9-yl-3-((S)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##