data_G4P # _chem_comp.id G4P _chem_comp.name "GUANOSINE-5',3'-TETRAPHOSPHATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H17 N5 O17 P4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "guanosine tetraphosphate;ppGpp" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2002-05-16 _chem_comp.pdbx_modified_date 2020-06-24 _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 603.160 _chem_comp.one_letter_code N _chem_comp.three_letter_code G4P _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1LNZ _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 G4P PB PB P 0 1 N N N 9.060 68.309 71.663 4.684 -4.187 -0.023 PB G4P 1 G4P O1B O1B O 0 1 N N N 8.231 69.237 72.448 4.172 -4.147 1.365 O1B G4P 2 G4P O2B O2B O 0 1 N N N 8.949 68.266 70.190 4.940 -5.716 -0.457 O2B G4P 3 G4P O3B O3B O 0 1 N N N 10.582 68.480 71.740 6.067 -3.367 -0.109 O3B G4P 4 G4P O3A O3A O 0 1 N N N 8.518 66.775 72.067 3.603 -3.522 -1.014 O3A G4P 5 G4P PA PA P 0 1 N N S 8.407 66.284 73.590 3.099 -2.165 -0.308 PA G4P 6 G4P O1A O1A O 0 1 N N N 9.338 65.150 73.418 2.938 -2.395 1.145 O1A G4P 7 G4P O2A O2A O 0 1 N N N 8.707 67.255 74.678 4.183 -0.999 -0.551 O2A G4P 8 G4P "O5'" O5* O 0 1 N N N 6.958 65.650 73.573 1.686 -1.724 -0.942 "O5'" G4P 9 G4P "C5'" C5* C 0 1 N N N 5.728 66.309 73.723 1.237 -0.589 -0.199 "C5'" G4P 10 G4P "C4'" C4* C 0 1 N N R 4.762 65.419 74.549 -0.109 -0.117 -0.753 "C4'" G4P 11 G4P "O4'" O4* O 0 1 N N N 4.119 64.328 73.814 -1.129 -1.110 -0.510 "O4'" G4P 12 G4P "C3'" C3* C 0 1 N N S 5.379 64.616 75.794 -0.594 1.140 0.004 "C3'" G4P 13 G4P "O3'" O3* O 0 1 N N N 4.626 65.017 76.965 -0.281 2.322 -0.736 "O3'" G4P 14 G4P "C2'" C2* C 0 1 N N R 5.183 63.104 75.525 -2.126 0.951 0.104 "C2'" G4P 15 G4P "O2'" O2* O 0 1 N N N 4.584 62.437 76.653 -2.806 2.013 -0.569 "O2'" G4P 16 G4P "C1'" C1* C 0 1 N N R 4.287 63.043 74.351 -2.382 -0.399 -0.602 "C1'" G4P 17 G4P N9 N9 N 0 1 Y N N 4.783 62.114 73.268 -3.442 -1.141 0.086 N9 G4P 18 G4P C8 C8 C 0 1 Y N N 5.920 62.060 72.496 -3.267 -2.078 1.063 C8 G4P 19 G4P N7 N7 N 0 1 Y N N 5.942 61.057 71.661 -4.423 -2.533 1.449 N7 G4P 20 G4P C5 C5 C 0 1 Y N N 4.765 60.395 71.858 -5.405 -1.919 0.745 C5 G4P 21 G4P C6 C6 C 0 1 N N N 4.188 59.210 71.264 -6.816 -2.010 0.738 C6 G4P 22 G4P O6 O6 O 0 1 N N N 4.657 58.509 70.396 -7.397 -2.778 1.486 O6 G4P 23 G4P N1 N1 N 0 1 N N N 2.907 58.854 71.769 -7.506 -1.221 -0.115 N1 G4P 24 G4P C2 C2 C 0 1 N N N 2.233 59.550 72.767 -6.847 -0.370 -0.952 C2 G4P 25 G4P N2 N2 N 0 1 N N N 1.056 59.075 73.134 -7.573 0.415 -1.812 N2 G4P 26 G4P N3 N3 N 0 1 N N N 2.769 60.689 73.368 -5.536 -0.276 -0.954 N3 G4P 27 G4P C4 C4 C 0 1 Y N N 4.007 61.025 72.851 -4.787 -1.022 -0.133 C4 G4P 28 G4P PC PC P 0 1 N N S 4.380 65.085 78.309 0.677 3.216 0.200 PC G4P 29 G4P O1C O1C O 0 1 N N N 4.591 63.855 79.137 1.848 2.413 0.617 O1C G4P 30 G4P O2C O2C O 0 1 N N N 3.045 65.740 78.340 -0.139 3.693 1.503 O2C G4P 31 G4P O3C O3C O 0 1 N N N 5.774 65.917 78.744 1.176 4.507 -0.623 O3C G4P 32 G4P PD PD P 0 1 N N N 5.792 67.631 78.985 2.495 5.052 0.123 PD G4P 33 G4P O1D O1D O 0 1 N N N 5.095 68.226 77.816 2.307 4.960 1.588 O1D G4P 34 G4P O2D O2D O 0 1 N N N 7.276 67.884 79.107 3.764 4.163 -0.312 O2D G4P 35 G4P O3D O3D O 0 1 N N N 5.369 68.126 80.417 2.749 6.588 -0.290 O3D G4P 36 G4P HOB2 2HOB H 0 0 N N N 8.032 68.257 69.941 5.591 -6.077 0.159 HOB2 G4P 37 G4P HOB3 3HOB H 0 0 N N N 10.942 68.515 70.862 6.365 -3.417 -1.027 HOB3 G4P 38 G4P HOA2 2HOA H 0 0 N N N 8.771 66.794 75.506 4.258 -0.882 -1.508 HOA2 G4P 39 G4P "H5'" 1H5* H 0 1 N N N 5.292 66.502 72.732 1.968 0.215 -0.286 "H5'" G4P 40 G4P "H5''" 2H5* H 0 0 N N N 5.885 67.264 74.246 1.122 -0.863 0.850 "H5''" G4P 41 G4P "H4'" H4* H 0 1 N N N 4.081 66.225 74.859 -0.028 0.091 -1.820 "H4'" G4P 42 G4P "H3'" H3* H 0 1 N N N 6.449 64.823 75.941 -0.148 1.183 0.998 "H3'" G4P 43 G4P "H2'" H2* H 0 1 N N N 6.144 62.597 75.351 -2.437 0.901 1.147 "H2'" G4P 44 G4P "HO2'" *HO2 H 0 0 N N N 4.452 61.519 76.445 -3.753 1.843 -0.474 "HO2'" G4P 45 G4P "H1'" H1* H 0 1 N N N 3.329 62.640 74.710 -2.651 -0.236 -1.646 "H1'" G4P 46 G4P H8 H8 H 0 1 N N N 6.721 62.781 72.574 -2.312 -2.394 1.457 H8 G4P 47 G4P HN1 HN1 H 0 1 N N N 2.460 58.048 71.380 -8.475 -1.266 -0.138 HN1 G4P 48 G4P HN21 1HN2 H 0 0 N N N 0.617 58.261 72.753 -7.119 1.028 -2.410 HN21 G4P 49 G4P HN22 2HN2 H 0 0 N N N 0.673 59.656 73.852 -8.541 0.353 -1.824 HN22 G4P 50 G4P H2C H2C H 0 1 N N N 2.781 65.880 79.242 -0.892 4.211 1.188 H2C G4P 51 G4P H2D H2D H 0 1 N N N 7.661 67.937 78.240 3.851 4.250 -1.271 H2D G4P 52 G4P H3D H3D H 0 1 N N N 5.284 67.379 80.998 3.546 6.874 0.177 H3D G4P 53 # # 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 G4P PB O1B DOUB N N 1 G4P PB O2B SING N N 2 G4P PB O3B SING N N 3 G4P PB O3A SING N N 4 G4P O2B HOB2 SING N N 5 G4P O3B HOB3 SING N N 6 G4P O3A PA SING N N 7 G4P PA O1A DOUB N N 8 G4P PA O2A SING N N 9 G4P PA "O5'" SING N N 10 G4P O2A HOA2 SING N N 11 G4P "O5'" "C5'" SING N N 12 G4P "C5'" "C4'" SING N N 13 G4P "C5'" "H5'" SING N N 14 G4P "C5'" "H5''" SING N N 15 G4P "C4'" "O4'" SING N N 16 G4P "C4'" "C3'" SING N N 17 G4P "C4'" "H4'" SING N N 18 G4P "O4'" "C1'" SING N N 19 G4P "C3'" "O3'" SING N N 20 G4P "C3'" "C2'" SING N N 21 G4P "C3'" "H3'" SING N N 22 G4P "O3'" PC SING N N 23 G4P "C2'" "O2'" SING N N 24 G4P "C2'" "C1'" SING N N 25 G4P "C2'" "H2'" SING N N 26 G4P "O2'" "HO2'" SING N N 27 G4P "C1'" N9 SING N N 28 G4P "C1'" "H1'" SING N N 29 G4P N9 C8 SING Y N 30 G4P N9 C4 SING Y N 31 G4P C8 N7 DOUB Y N 32 G4P C8 H8 SING N N 33 G4P N7 C5 SING Y N 34 G4P C5 C6 SING N N 35 G4P C5 C4 DOUB Y N 36 G4P C6 O6 DOUB N N 37 G4P C6 N1 SING N N 38 G4P N1 C2 SING N N 39 G4P N1 HN1 SING N N 40 G4P C2 N2 SING N N 41 G4P C2 N3 DOUB N N 42 G4P N2 HN21 SING N N 43 G4P N2 HN22 SING N N 44 G4P N3 C4 SING N N 45 G4P PC O1C DOUB N N 46 G4P PC O2C SING N N 47 G4P PC O3C SING N N 48 G4P O2C H2C SING N N 49 G4P O3C PD SING N N 50 G4P PD O1D DOUB N N 51 G4P PD O2D SING N N 52 G4P PD O3D SING N N 53 G4P O2D H2D SING N N 54 G4P O3D H3D SING N N 55 # # 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 G4P SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3OP(=O)(O)OP(=O)(O)O" G4P SMILES_CANONICAL CACTVS 3.341 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O[P@@](O)(=O)O[P](O)(O)=O)[C@H]3O" G4P SMILES CACTVS 3.341 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(=O)O[P](O)(O)=O)[CH]3O" G4P SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O[P@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N" G4P SMILES "OpenEye OEToolkits" 1.5.0 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N" G4P InChI InChI 1.03 "InChI=1S/C10H17N5O17P4/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(30-36(26,27)32-34(21,22)23)3(29-9)1-28-35(24,25)31-33(18,19)20/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1" G4P InChIKey InChI 1.03 BUFLLCUFNHESEH-UUOKFMHZSA-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 G4P "SYSTEMATIC NAME" ACDLabs 10.04 "guanosine 3',5'-bis(trihydrogen diphosphate)" G4P "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-4-hydroxy-3-(hydroxy-phosphonooxy-phosphoryl)oxy-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 G4P "Create component" 2002-05-16 RCSB G4P "Modify descriptor" 2011-06-04 RCSB G4P "Modify synonyms" 2020-06-24 PDBE # # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 G4P "guanosine tetraphosphate" ? ? 2 G4P ppGpp ? ? ##