data_8GD # _chem_comp.id 8GD _chem_comp.name "2'-deoxy-8-oxoguanosine 5'-(trihydrogen diphosphate)" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H15 N5 O11 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "8-oxo-7,8-dihydro-2'-deoxy-guanosine-5'-diphosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-01-09 _chem_comp.pdbx_modified_date 2021-03-13 _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 443.201 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 8GD _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 3AC9 _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 8GD N1 N1 N 0 1 N N N -18.192 22.624 78.146 -6.205 1.971 0.364 N1 8GD 1 8GD C2 C2 C 0 1 N N N -18.256 21.427 77.469 -5.560 1.533 1.480 C2 8GD 2 8GD N2 N2 N 0 1 N N N -17.109 20.959 76.949 -6.022 1.918 2.713 N2 8GD 3 8GD N3 N3 N 0 1 N N N -19.374 20.733 77.315 -4.505 0.751 1.407 N3 8GD 4 8GD C4 C4 C 0 1 N N N -20.436 21.347 77.898 -4.022 0.352 0.225 C4 8GD 5 8GD C5 C5 C 0 1 N N N -20.472 22.536 78.585 -4.642 0.770 -0.946 C5 8GD 6 8GD C6 C6 C 0 1 N N N -19.276 23.265 78.745 -5.766 1.604 -0.861 C6 8GD 7 8GD O6 O6 O 0 1 N N N -19.116 24.342 79.328 -6.336 1.988 -1.869 O6 8GD 8 8GD N7 N7 N 0 1 N N N -21.758 22.811 79.018 -3.930 0.206 -2.008 N7 8GD 9 8GD C8 C8 C 0 1 N N N -22.482 21.805 78.598 -2.921 -0.522 -1.489 C8 8GD 10 8GD O8 O8 O 0 1 N N N -23.692 21.742 78.822 -2.103 -1.150 -2.135 O8 8GD 11 8GD N9 N9 N 0 1 N N N -21.728 20.879 77.907 -2.959 -0.447 -0.146 N9 8GD 12 8GD PA PA P 0 1 N N N -23.546 19.018 71.774 3.743 -0.566 -0.203 PA 8GD 13 8GD PB PB P 0 1 N N N -25.834 17.918 73.282 5.523 1.778 0.146 PB 8GD 14 8GD "C1'" "C1'" C 0 1 N N R -22.131 19.617 77.260 -2.026 -1.105 0.772 "C1'" 8GD 15 8GD O1A O1A O 0 1 N N N -23.452 18.326 70.463 3.621 -0.304 -1.655 O1A 8GD 16 8GD O1B O1B O 0 1 N N N -26.638 18.043 72.058 6.962 1.085 0.352 O1B 8GD 17 8GD "C2'" "C2'" C 0 1 N N N -23.557 19.621 76.739 -2.172 -2.635 0.660 "C2'" 8GD 18 8GD O2A O2A O 0 1 N N N -24.145 20.390 71.822 4.710 -1.831 0.034 O2A 8GD 19 8GD O2B O2B O 0 1 N N N -26.090 18.797 74.400 5.372 2.190 -1.267 O2B 8GD 20 8GD "C3'" "C3'" C 0 1 N N S -23.459 18.647 75.571 -0.759 -3.122 0.256 "C3'" 8GD 21 8GD "O3'" "O3'" O 0 1 N N N -23.516 17.312 76.064 -0.412 -4.318 0.958 "O3'" 8GD 22 8GD O3A O3A O 0 1 N N N -24.319 18.009 72.807 4.363 0.728 0.526 O3A 8GD 23 8GD O3B O3B O 0 1 N N N -25.973 16.426 73.804 5.409 3.071 1.098 O3B 8GD 24 8GD "C4'" "C4'" C 0 1 N N R -22.058 18.895 75.008 0.134 -1.938 0.705 "C4'" 8GD 25 8GD "O4'" "O4'" O 0 1 N N N -21.293 19.439 76.117 -0.673 -0.777 0.412 "O4'" 8GD 26 8GD "C5'" "C5'" C 0 1 N N N -21.990 19.788 73.770 1.434 -1.908 -0.102 "C5'" 8GD 27 8GD "O5'" "O5'" O 0 1 N N N -22.167 18.981 72.578 2.287 -0.881 0.409 "O5'" 8GD 28 8GD HN1 HN1 H 0 1 N N N -17.299 23.068 78.213 -6.983 2.544 0.448 HN1 8GD 29 8GD HN2 HN2 H 0 1 N N N -17.103 20.092 76.450 -6.799 2.495 2.782 HN2 8GD 30 8GD HN2A HN2A H 0 0 N N N -16.261 21.477 77.061 -5.571 1.614 3.517 HN2A 8GD 31 8GD HN7 HN7 H 0 1 N N N -22.067 23.607 79.539 -4.127 0.318 -2.951 HN7 8GD 32 8GD "H1'" "H1'" H 0 1 N N N -22.046 18.826 78.019 -2.226 -0.787 1.795 "H1'" 8GD 33 8GD HO1B HO1B H 0 0 N N N -27.274 18.741 72.166 7.130 0.789 1.257 HO1B 8GD 34 8GD "H2'" "H2'" H 0 1 N N N -24.278 19.287 77.499 -2.462 -3.061 1.620 "H2'" 8GD 35 8GD "H2'A" "H2'A" H 0 0 N N N -23.879 20.623 76.419 -2.900 -2.893 -0.109 "H2'A" 8GD 36 8GD HO2A HO2A H 0 0 N N N -24.403 20.654 70.947 4.836 -2.061 0.965 HO2A 8GD 37 8GD "H3'" "H3'" H 0 1 N N N -24.263 18.782 74.833 -0.694 -3.273 -0.822 "H3'" 8GD 38 8GD "HO3'" "HO3'" H 0 0 N N N -23.455 16.703 75.338 -1.000 -5.064 0.778 "HO3'" 8GD 39 8GD HO3B HO3B H 0 0 N N N -26.192 16.433 74.728 6.079 3.747 0.925 HO3B 8GD 40 8GD "H4'" "H4'" H 0 1 N N N -21.648 17.948 74.626 0.345 -1.999 1.772 "H4'" 8GD 41 8GD "H5'" "H5'" H 0 1 N N N -22.786 20.545 73.821 1.935 -2.872 -0.019 "H5'" 8GD 42 8GD "H5'A" "H5'A" H 0 0 N N N -21.010 20.287 73.732 1.207 -1.705 -1.148 "H5'A" 8GD 43 # # 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 8GD N1 C2 SING N N 1 8GD N1 C6 SING N N 2 8GD C2 N2 SING N N 3 8GD C2 N3 DOUB N N 4 8GD N3 C4 SING N N 5 8GD C4 C5 DOUB N N 6 8GD C4 N9 SING N N 7 8GD C5 C6 SING N N 8 8GD C5 N7 SING N N 9 8GD C6 O6 DOUB N N 10 8GD N7 C8 SING N N 11 8GD C8 O8 DOUB N N 12 8GD C8 N9 SING N N 13 8GD N9 "C1'" SING N N 14 8GD PA O1A DOUB N N 15 8GD PA O2A SING N N 16 8GD PA O3A SING N N 17 8GD PA "O5'" SING N N 18 8GD PB O1B SING N N 19 8GD PB O2B DOUB N N 20 8GD PB O3A SING N N 21 8GD PB O3B SING N N 22 8GD "C1'" "C2'" SING N N 23 8GD "C1'" "O4'" SING N N 24 8GD "C2'" "C3'" SING N N 25 8GD "C3'" "O3'" SING N N 26 8GD "C3'" "C4'" SING N N 27 8GD "C4'" "O4'" SING N N 28 8GD "C4'" "C5'" SING N N 29 8GD "C5'" "O5'" SING N N 30 8GD N1 HN1 SING N N 31 8GD N2 HN2 SING N N 32 8GD N2 HN2A SING N N 33 8GD N7 HN7 SING N N 34 8GD "C1'" "H1'" SING N N 35 8GD O1B HO1B SING N N 36 8GD "C2'" "H2'" SING N N 37 8GD "C2'" "H2'A" SING N N 38 8GD O2A HO2A SING N N 39 8GD "C3'" "H3'" SING N N 40 8GD "O3'" "HO3'" SING N N 41 8GD O3B HO3B SING N N 42 8GD "C4'" "H4'" SING N N 43 8GD "C5'" "H5'" SING N N 44 8GD "C5'" "H5'A" SING N N 45 # # 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 8GD SMILES_CANONICAL CACTVS 3.352 "NC1=NC2=C(NC(=O)N2[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(O)=O)O3)C(=O)N1" 8GD SMILES CACTVS 3.352 "NC1=NC2=C(NC(=O)N2[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O3)C(=O)N1" 8GD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1[C@@H]([C@H](O[C@H]1N2C3=C(C(=O)NC(=N3)N)NC2=O)CO[P@](=O)(O)OP(=O)(O)O)O" 8GD SMILES "OpenEye OEToolkits" 1.7.0 "C1C(C(OC1N2C3=C(C(=O)NC(=N3)N)NC2=O)COP(=O)(O)OP(=O)(O)O)O" 8GD InChI InChI 1.03 "InChI=1S/C10H15N5O11P2/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(25-5)2-24-28(22,23)26-27(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1" 8GD InChIKey InChI 1.03 LJMLTZSNWOCYNQ-VPENINKCSA-N # _pdbx_chem_comp_identifier.comp_id 8GD _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 1.6.1 _pdbx_chem_comp_identifier.identifier "[(2R,3S,5R)-5-(2-azanyl-6,8-dioxo-1,7-dihydropurin-9-yl)-3-hydroxy-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 8GD "Create component" 2010-01-09 PDBJ 8GD "Modify descriptor" 2011-06-04 RCSB 8GD "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 8GD _pdbx_chem_comp_synonyms.name "8-oxo-7,8-dihydro-2'-deoxy-guanosine-5'-diphosphate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##