data_GDP # _chem_comp.id GDP _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H15 N5 O11 P2" _chem_comp.mon_nstd_parent_comp_id G _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2014-05-12 _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 G _chem_comp.three_letter_code GDP _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 1EK0 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 GDP PB PB P 0 1 N N N 13.635 17.027 28.402 -5.743 -1.471 0.475 PB GDP 1 GDP O1B O1B O 0 1 N N N 14.317 18.299 28.131 -6.829 -0.831 -0.300 O1B GDP 2 GDP O2B O2B O 0 1 N N N 14.465 15.868 28.851 -6.293 -1.885 1.930 O2B GDP 3 GDP O3B O3B O 0 1 N N N 12.657 17.014 29.609 -5.234 -2.787 -0.301 O3B GDP 4 GDP O3A O3A O 0 1 N N N 13.031 16.438 26.904 -4.519 -0.438 0.638 O3A GDP 5 GDP PA PA P 0 1 N N N 12.164 17.382 25.843 -3.821 0.633 -0.340 PA GDP 6 GDP O1A O1A O 0 1 N N N 11.308 16.310 25.239 -3.718 0.063 -1.702 O1A GDP 7 GDP O2A O2A O 0 1 N N N 11.654 18.737 26.082 -4.708 1.976 -0.386 O2A GDP 8 GDP "O5'" "O5'" O 0 1 N N N 13.417 17.470 24.852 -2.348 0.981 0.208 "O5'" GDP 9 GDP "C5'" "C5'" C 0 1 N N N 14.543 18.324 25.037 -1.434 1.823 -0.497 "C5'" GDP 10 GDP "C4'" "C4'" C 0 1 N N R 15.043 18.710 23.648 -0.133 1.943 0.299 "C4'" GDP 11 GDP "O4'" "O4'" O 0 1 N N N 15.183 17.536 22.793 0.533 0.670 0.344 "O4'" GDP 12 GDP "C3'" "C3'" C 0 1 N N S 13.926 19.400 22.829 0.820 2.933 -0.399 "C3'" GDP 13 GDP "O3'" "O3'" O 0 1 N N N 14.002 20.787 23.226 1.125 4.028 0.467 "O3'" GDP 14 GDP "C2'" "C2'" C 0 1 N N R 14.511 19.303 21.406 2.091 2.098 -0.686 "C2'" GDP 15 GDP "O2'" "O2'" O 0 1 N N N 15.627 20.165 21.220 3.271 2.861 -0.428 "O2'" GDP 16 GDP "C1'" "C1'" C 0 1 N N R 15.015 17.874 21.438 1.952 0.935 0.329 "C1'" GDP 17 GDP N9 N9 N 0 1 Y N N 13.968 16.928 20.922 2.691 -0.243 -0.132 N9 GDP 18 GDP C8 C8 C 0 1 Y N N 13.129 16.056 21.555 2.200 -1.252 -0.908 C8 GDP 19 GDP N7 N7 N 0 1 Y N N 12.358 15.405 20.737 3.131 -2.134 -1.125 N7 GDP 20 GDP C5 C5 C 0 1 Y N N 12.701 15.869 19.474 4.272 -1.746 -0.504 C5 GDP 21 GDP C6 C6 C 0 1 N N N 12.214 15.545 18.183 5.571 -2.295 -0.396 C6 GDP 22 GDP O6 O6 O 0 1 N N N 11.326 14.728 17.882 5.850 -3.350 -0.939 O6 GDP 23 GDP N1 N1 N 0 1 N N N 12.870 16.282 17.187 6.495 -1.620 0.324 N1 GDP 24 GDP C2 C2 C 0 1 N N N 13.858 17.205 17.402 6.171 -0.441 0.927 C2 GDP 25 GDP N2 N2 N 0 1 N N N 14.348 17.795 16.316 7.130 0.222 1.651 N2 GDP 26 GDP N3 N3 N 0 1 N N N 14.329 17.524 18.614 4.968 0.079 0.834 N3 GDP 27 GDP C4 C4 C 0 1 Y N N 13.701 16.819 19.565 4.003 -0.529 0.133 C4 GDP 28 GDP HOB2 HOB2 H 0 0 N N N 15.376 16.131 28.902 -7.033 -2.508 1.908 HOB2 GDP 29 GDP HOB3 HOB3 H 0 0 N N N 12.643 17.873 30.015 -4.521 -3.259 0.151 HOB3 GDP 30 GDP HOA2 HOA2 H 0 0 N N N 10.749 18.789 25.799 -4.818 2.404 0.474 HOA2 GDP 31 GDP "H5'" "H5'1" H 0 1 N N N 14.247 19.224 25.596 -1.222 1.390 -1.475 "H5'" GDP 32 GDP "H5''" "H5'2" H 0 0 N N N 15.333 17.793 25.589 -1.874 2.811 -0.625 "H5''" GDP 33 GDP "H4'" "H4'" H 0 1 N N N 15.955 19.324 23.692 -0.349 2.285 1.312 "H4'" GDP 34 GDP "H3'" "H3'" H 0 1 N N N 12.939 18.927 22.938 0.380 3.294 -1.329 "H3'" GDP 35 GDP "HO3'" "HO3'" H 0 0 N Y N 13.340 21.286 22.762 1.722 4.683 0.078 "HO3'" GDP 36 GDP "H2'" "H2'" H 0 1 N N N 13.729 19.439 20.644 2.088 1.724 -1.710 "H2'" GDP 37 GDP "HO2'" "HO2'" H 0 0 N N N 15.954 20.073 20.333 3.357 3.652 -0.979 "HO2'" GDP 38 GDP "H1'" "H1'" H 0 1 N N N 15.948 17.778 20.863 2.295 1.244 1.316 "H1'" GDP 39 GDP H8 H8 H 0 1 N N N 13.109 15.921 22.626 1.190 -1.310 -1.285 H8 GDP 40 GDP HN1 HN1 H 0 1 N N N 12.593 16.120 16.240 7.392 -1.977 0.412 HN1 GDP 41 GDP HN21 HN21 H 0 0 N N N 15.071 18.480 16.402 8.023 -0.150 1.728 HN21 GDP 42 GDP HN22 HN22 H 0 0 N N N 13.993 17.554 15.413 6.915 1.062 2.086 HN22 GDP 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 GDP PB O1B DOUB N N 1 GDP PB O2B SING N N 2 GDP PB O3B SING N N 3 GDP PB O3A SING N N 4 GDP O2B HOB2 SING N N 5 GDP O3B HOB3 SING N N 6 GDP O3A PA SING N N 7 GDP PA O1A DOUB N N 8 GDP PA O2A SING N N 9 GDP PA "O5'" SING N N 10 GDP O2A HOA2 SING N N 11 GDP "O5'" "C5'" SING N N 12 GDP "C5'" "C4'" SING N N 13 GDP "C5'" "H5'" SING N N 14 GDP "C5'" "H5''" SING N N 15 GDP "C4'" "O4'" SING N N 16 GDP "C4'" "C3'" SING N N 17 GDP "C4'" "H4'" SING N N 18 GDP "O4'" "C1'" SING N N 19 GDP "C3'" "O3'" SING N N 20 GDP "C3'" "C2'" SING N N 21 GDP "C3'" "H3'" SING N N 22 GDP "O3'" "HO3'" SING N N 23 GDP "C2'" "O2'" SING N N 24 GDP "C2'" "C1'" SING N N 25 GDP "C2'" "H2'" SING N N 26 GDP "O2'" "HO2'" SING N N 27 GDP "C1'" N9 SING N N 28 GDP "C1'" "H1'" SING N N 29 GDP N9 C8 SING Y N 30 GDP N9 C4 SING Y N 31 GDP C8 N7 DOUB Y N 32 GDP C8 H8 SING N N 33 GDP N7 C5 SING Y N 34 GDP C5 C6 SING N N 35 GDP C5 C4 DOUB Y N 36 GDP C6 O6 DOUB N N 37 GDP C6 N1 SING N N 38 GDP N1 C2 SING N N 39 GDP N1 HN1 SING N N 40 GDP C2 N2 SING N N 41 GDP C2 N3 DOUB N N 42 GDP N2 HN21 SING N N 43 GDP N2 HN22 SING N N 44 GDP N3 C4 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 GDP SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O" GDP InChI InChI 1.03 "InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1" GDP InChIKey InChI 1.03 QGWNDRXFNXRZMB-UUOKFMHZSA-N GDP SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O" GDP SMILES CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O" GDP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N" GDP SMILES "OpenEye OEToolkits" 1.7.6 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N" # # 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 GDP "SYSTEMATIC NAME" ACDLabs 12.01 "guanosine 5'-(trihydrogen diphosphate)" GDP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-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 GDP "Create component" 1999-07-08 EBI GDP "Modify descriptor" 2011-06-04 RCSB GDP "Other modification" 2014-05-12 RCSB ##