data_G8D # _chem_comp.id G8D _chem_comp.name ;[(2R,3S,4R,5R)-5-[2-azanyl-6,8-bis(oxidanylidene)-1,7-dihydropurin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H15 N5 O12 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "8-oxoguanosine-5'-diphosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-06-17 _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 459.200 _chem_comp.one_letter_code ? _chem_comp.three_letter_code G8D _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 5GGA _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 G8D O3B O1 O 0 1 N N N 18.547 15.917 25.411 6.874 0.258 1.347 O3B G8D 1 G8D PB P1 P 0 1 N N N 19.380 17.188 25.446 5.948 1.356 0.620 PB G8D 2 G8D O2B O2 O 0 1 N N N 19.506 17.844 26.826 5.933 2.709 1.493 O2B G8D 3 G8D O1B O3 O 0 1 N N N 19.014 18.131 24.330 6.489 1.644 -0.727 O1B G8D 4 G8D O3A O4 O 0 1 N N N 20.928 16.681 25.255 4.447 0.789 0.485 O3A G8D 5 G8D PA P2 P 0 1 N N N 21.736 16.071 23.953 3.746 -0.302 -0.469 PA G8D 6 G8D O1A O5 O 0 1 N N N 21.167 16.421 22.605 4.603 -1.506 -0.556 O1A G8D 7 G8D O2A O6 O 0 1 N N N 22.260 14.648 24.188 3.546 0.321 -1.940 O2A G8D 8 G8D "O5'" O7 O 0 1 N N N 23.078 17.005 24.072 2.312 -0.707 0.142 "O5'" G8D 9 G8D "C5'" C1 C 0 1 N N N 23.839 17.079 25.274 1.488 -1.731 -0.419 "C5'" G8D 10 G8D "C4'" C2 C 0 1 N N R 25.234 17.383 24.813 0.203 -1.858 0.401 "C4'" G8D 11 G8D "O4'" O8 O 0 1 N N N 25.700 16.240 24.082 -0.588 -0.666 0.257 "O4'" G8D 12 G8D "C3'" C3 C 0 1 N N S 25.278 18.543 23.821 -0.639 -3.037 -0.123 "C3'" G8D 13 G8D "O3'" O9 O 0 1 N N N 26.263 19.474 24.235 -0.835 -4.008 0.907 "O3'" G8D 14 G8D "C2'" C4 C 0 1 N N R 25.723 17.960 22.488 -1.988 -2.392 -0.523 "C2'" G8D 15 G8D "O2'" O10 O 0 1 N N N 26.586 18.871 21.754 -3.086 -3.220 -0.136 "O2'" G8D 16 G8D "C1'" C5 C 0 1 N N R 26.435 16.679 22.938 -1.973 -1.072 0.298 "C1'" G8D 17 G8D N9 N1 N 0 1 N N N 26.495 15.570 21.946 -2.827 -0.063 -0.332 N9 G8D 18 G8D C8 C6 C 0 1 N N N 27.467 14.618 21.854 -2.618 0.500 -1.537 C8 G8D 19 G8D O8 O11 O 0 1 N N N 28.638 14.549 22.746 -1.686 0.248 -2.278 O8 G8D 20 G8D C4 C7 C 0 1 N N N 25.598 15.296 20.976 -3.982 0.464 0.209 C4 G8D 21 G8D N3 N2 N 0 1 N N N 24.423 15.870 20.571 -4.638 0.258 1.357 N3 G8D 22 G8D C2 C8 C 0 1 N N N 23.764 15.306 19.507 -5.746 0.910 1.633 C2 G8D 23 G8D N2 N3 N 0 1 N N N 22.601 15.801 19.042 -6.386 0.669 2.822 N2 G8D 24 G8D N1 N4 N 0 1 N N N 24.199 14.198 18.828 -6.275 1.820 0.768 N1 G8D 25 G8D C6 C9 C 0 1 N N N 25.333 13.538 19.127 -5.660 2.073 -0.409 C6 G8D 26 G8D O6 O12 O 0 1 N N N 25.666 12.518 18.437 -6.124 2.887 -1.192 O6 G8D 27 G8D C5 C10 C 0 1 N N N 26.135 14.075 20.279 -4.478 1.381 -0.709 C5 G8D 28 G8D N7 N5 N 0 1 N N N 27.317 13.704 20.875 -3.602 1.384 -1.797 N7 G8D 29 G8D H1 H1 H 0 1 N N N 17.941 15.955 24.680 6.577 0.020 2.236 H1 G8D 30 G8D H2 H2 H 0 1 N N N 19.326 18.774 26.753 6.806 3.107 1.615 H2 G8D 31 G8D H3 H3 H 0 1 N N N 22.150 14.135 23.396 2.993 1.114 -1.959 H3 G8D 32 G8D H4 H4 H 0 1 N N N 23.461 17.880 25.926 1.239 -1.474 -1.448 H4 G8D 33 G8D H5 H5 H 0 1 N N N 23.807 16.121 25.814 2.025 -2.680 -0.401 H5 G8D 34 G8D H6 H6 H 0 1 N N N 25.883 17.600 25.674 0.448 -2.015 1.452 H6 G8D 35 G8D H7 H7 H 0 1 N N N 24.285 19.006 23.727 -0.160 -3.493 -0.989 H7 G8D 36 G8D H8 H8 H 0 1 N N N 26.010 19.855 25.068 -1.359 -4.773 0.632 H8 G8D 37 G8D H9 H9 H 0 1 N N N 24.840 17.696 21.887 -2.017 -2.184 -1.592 H9 G8D 38 G8D H10 H10 H 0 1 N N N 26.092 19.643 21.503 -3.138 -4.056 -0.621 H10 G8D 39 G8D H11 H11 H 0 1 N N N 27.460 16.942 23.237 -2.288 -1.256 1.326 H11 G8D 40 G8D H12 H12 H 0 1 N N N 22.191 16.604 19.474 -6.021 0.023 3.447 H12 G8D 41 G8D H13 H13 H 0 1 N N N 22.147 15.365 18.265 -7.205 1.143 3.037 H13 G8D 42 G8D H14 H14 H 0 1 N N N 23.643 13.861 18.068 -7.094 2.286 0.997 H14 G8D 43 G8D H15 H15 H 0 1 N N N 27.919 12.941 20.639 -3.687 1.924 -2.598 H15 G8D 44 # # 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 G8D O6 C6 DOUB N N 1 G8D N1 C6 SING N N 2 G8D N1 C2 SING N N 3 G8D N2 C2 SING N N 4 G8D C6 C5 SING N N 5 G8D C2 N3 DOUB N N 6 G8D C5 N7 SING N N 7 G8D C5 C4 DOUB N N 8 G8D N3 C4 SING N N 9 G8D N7 C8 SING N N 10 G8D C4 N9 SING N N 11 G8D "O2'" "C2'" SING N N 12 G8D C8 N9 SING N N 13 G8D C8 O8 DOUB N N 14 G8D N9 "C1'" SING N N 15 G8D "C2'" "C1'" SING N N 16 G8D "C2'" "C3'" SING N N 17 G8D O1A PA DOUB N N 18 G8D "C1'" "O4'" SING N N 19 G8D "C3'" "O3'" SING N N 20 G8D "C3'" "C4'" SING N N 21 G8D PA "O5'" SING N N 22 G8D PA O2A SING N N 23 G8D PA O3A SING N N 24 G8D "O5'" "C5'" SING N N 25 G8D "O4'" "C4'" SING N N 26 G8D O1B PB DOUB N N 27 G8D "C4'" "C5'" SING N N 28 G8D O3A PB SING N N 29 G8D O3B PB SING N N 30 G8D PB O2B SING N N 31 G8D O3B H1 SING N N 32 G8D O2B H2 SING N N 33 G8D O2A H3 SING N N 34 G8D "C5'" H4 SING N N 35 G8D "C5'" H5 SING N N 36 G8D "C4'" H6 SING N N 37 G8D "C3'" H7 SING N N 38 G8D "O3'" H8 SING N N 39 G8D "C2'" H9 SING N N 40 G8D "O2'" H10 SING N N 41 G8D "C1'" H11 SING N N 42 G8D N2 H12 SING N N 43 G8D N2 H13 SING N N 44 G8D N1 H14 SING N N 45 G8D N7 H15 SING N N 46 # # 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 G8D InChI InChI 1.03 "InChI=1S/C10H15N5O12P2/c11-9-13-6-3(7(18)14-9)12-10(19)15(6)8-5(17)4(16)2(26-8)1-25-29(23,24)27-28(20,21)22/h2,4-5,8,16-17H,1H2,(H,12,19)(H,23,24)(H2,20,21,22)(H3,11,13,14,18)/t2-,4-,5-,8-/m1/s1" G8D InChIKey InChI 1.03 PQVZQFDCRLHZRP-UMMCILCDSA-N G8D SMILES_CANONICAL CACTVS 3.385 "NC1=NC2=C(NC(=O)N2[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O)C(=O)N1" G8D SMILES CACTVS 3.385 "NC1=NC2=C(NC(=O)N2[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O)C(=O)N1" G8D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.5 "C([C@@H]1[C@H]([C@H]([C@@H](O1)N2C3=C(C(=O)NC(=N3)N)NC2=O)O)O)OP(=O)(O)OP(=O)(O)O" G8D SMILES "OpenEye OEToolkits" 2.0.5 "C(C1C(C(C(O1)N2C3=C(C(=O)NC(=N3)N)NC2=O)O)O)OP(=O)(O)OP(=O)(O)O" # _pdbx_chem_comp_identifier.comp_id G8D _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.5 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-6,8-bis(oxidanylidene)-1,7-dihydropurin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen 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 G8D "Create component" 2016-06-17 PDBJ G8D "Initial release" 2017-04-19 RCSB G8D "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id G8D _pdbx_chem_comp_synonyms.name "8-oxoguanosine-5'-diphosphate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##