data_AGS # _chem_comp.id AGS _chem_comp.name "PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H16 N5 O12 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 "SAP,ATG" _chem_comp.formula_weight 523.247 _chem_comp.one_letter_code ? _chem_comp.three_letter_code AGS _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 1MMG _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 AGS PG PG P 0 1 N N N 19.268 31.770 23.126 -5.637 -2.115 0.586 PG AGS 1 AGS S1G S1G S 0 1 N N N 21.065 32.639 23.413 -7.391 -1.534 0.347 S1G AGS 2 AGS O2G O2G O 0 1 N N N 18.713 31.367 24.546 -5.542 -2.991 1.934 O2G AGS 3 AGS O3G O3G O 0 1 N N N 19.419 30.562 22.220 -5.194 -3.016 -0.672 O3G AGS 4 AGS PB PB P 0 1 N N N 17.866 33.370 21.089 -4.304 0.389 -0.272 PB AGS 5 AGS O1B O1B O 0 1 N N N 18.381 34.736 20.924 -4.199 -0.101 -1.664 O1B AGS 6 AGS O2B O2B O 0 1 N N N 18.364 32.276 20.112 -5.464 1.501 -0.180 O2B AGS 7 AGS O3B O3B O 0 1 N N N 18.173 32.841 22.584 -4.661 -0.841 0.705 O3B AGS 8 AGS PA PA P 0 1 N N N 15.223 32.680 20.323 -1.862 2.050 -0.526 PA AGS 9 AGS O1A O1A O 0 1 N N N 15.301 32.939 18.769 -1.736 1.711 -1.961 O1A AGS 10 AGS O2A O2A O 0 1 N N N 15.270 31.169 20.572 -2.400 3.561 -0.377 O2A AGS 11 AGS O3A O3A O 0 1 N N N 16.296 33.429 21.145 -2.901 1.039 0.176 O3A AGS 12 AGS "O5'" "O5'" O 0 1 N N N 13.895 33.409 20.870 -0.424 1.920 0.185 "O5'" AGS 13 AGS "C5'" "C5'" C 0 1 N N N 13.156 32.787 21.952 0.738 2.612 -0.278 "C5'" AGS 14 AGS "C4'" "C4'" C 0 1 N N R 11.671 32.879 21.645 1.928 2.266 0.620 "C4'" AGS 15 AGS "O4'" "O4'" O 0 1 N N N 11.338 34.239 21.298 2.268 0.878 0.468 "O4'" AGS 16 AGS "C3'" "C3'" C 0 1 N N S 11.203 32.098 20.420 3.160 3.089 0.196 "C3'" AGS 17 AGS "O3'" "O3'" O 0 1 N N N 11.227 30.645 20.593 3.609 3.911 1.276 "O3'" AGS 18 AGS "C2'" "C2'" C 0 1 N N R 9.870 32.845 20.212 4.227 2.023 -0.153 "C2'" AGS 19 AGS "O2'" "O2'" O 0 1 N N N 8.853 32.591 21.205 5.514 2.411 0.331 "O2'" AGS 20 AGS "C1'" "C1'" C 0 1 N N R 10.315 34.261 20.396 3.702 0.778 0.607 "C1'" AGS 21 AGS N9 N9 N 0 1 Y N N 10.700 34.897 19.153 4.195 -0.453 -0.016 N9 AGS 22 AGS C8 C8 C 0 1 Y N N 11.902 35.271 18.665 3.578 -1.161 -1.004 C8 AGS 23 AGS N7 N7 N 0 1 Y N N 11.791 36.062 17.588 4.295 -2.200 -1.321 N7 AGS 24 AGS C5 C5 C 0 1 Y N N 10.424 36.081 17.338 5.414 -2.225 -0.558 C5 AGS 25 AGS C6 C6 C 0 1 Y N N 9.656 36.702 16.326 6.523 -3.083 -0.458 C6 AGS 26 AGS N6 N6 N 0 1 N N N 10.064 37.403 15.377 6.627 -4.202 -1.266 N6 AGS 27 AGS N1 N1 N 0 1 Y N N 8.322 36.453 16.468 7.469 -2.794 0.429 N1 AGS 28 AGS C2 C2 C 0 1 Y N N 7.752 35.743 17.494 7.378 -1.728 1.204 C2 AGS 29 AGS N3 N3 N 0 1 Y N N 8.432 35.156 18.440 6.358 -0.898 1.145 N3 AGS 30 AGS C4 C4 C 0 1 Y N N 9.762 35.345 18.288 5.367 -1.102 0.284 C4 AGS 31 AGS HOG2 HOG2 H 0 0 N N N 19.339 31.619 25.214 -6.105 -3.777 1.933 HOG2 AGS 32 AGS H21 H21 H 0 1 N N N 20.331 30.463 21.973 -4.290 -3.354 -0.615 H21 AGS 33 AGS HOB2 HOB2 H 0 0 N N N 18.977 32.657 19.494 -5.589 1.867 0.706 HOB2 AGS 34 AGS HOA2 HOA2 H 0 0 N N N 15.336 30.713 19.741 -2.507 3.852 0.539 HOA2 AGS 35 AGS "H5'1" "H5'1" H 0 0 N N N 13.450 31.731 22.042 0.956 2.311 -1.302 "H5'1" AGS 36 AGS "H5'2" "H5'2" H 0 0 N N N 13.372 33.309 22.896 0.558 3.687 -0.245 "H5'2" AGS 37 AGS "H4'" "H4'" H 0 1 N N N 11.096 32.555 22.525 1.681 2.476 1.661 "H4'" AGS 38 AGS "H3'" "H3'" H 0 1 N N N 11.865 32.361 19.582 2.929 3.700 -0.677 "H3'" AGS 39 AGS "HO3'" "HO3'" H 0 0 N N N 10.925 30.226 19.796 4.383 4.450 1.064 "HO3'" AGS 40 AGS "H2'" "H2'" H 0 1 N N N 9.494 32.679 19.191 4.257 1.839 -1.227 "H2'" AGS 41 AGS "HO2'" "HO2'" H 0 0 N N N 8.073 33.091 20.995 5.845 3.235 -0.050 "HO2'" AGS 42 AGS "H1'" "H1'" H 0 1 N N N 9.469 34.822 20.820 3.990 0.820 1.657 "H1'" AGS 43 AGS H8 H8 H 0 1 N N N 12.846 34.968 19.093 2.634 -0.898 -1.457 H8 AGS 44 AGS HN61 HN61 H 0 0 N N N 9.287 37.698 14.822 5.930 -4.402 -1.910 HN61 AGS 45 AGS HN62 HN62 H 0 0 N N N 10.541 38.205 15.736 7.398 -4.786 -1.188 HN62 AGS 46 AGS H2 H2 H 0 1 N N N 6.675 35.665 17.520 8.169 -1.531 1.912 H2 AGS 47 # # 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 AGS PG S1G DOUB N N 1 AGS PG O2G SING N N 2 AGS PG O3G SING N N 3 AGS PG O3B SING N N 4 AGS PB O1B DOUB N N 5 AGS PB O2B SING N N 6 AGS PB O3B SING N N 7 AGS PB O3A SING N N 8 AGS PA O1A DOUB N N 9 AGS PA O2A SING N N 10 AGS PA O3A SING N N 11 AGS PA "O5'" SING N N 12 AGS "O5'" "C5'" SING N N 13 AGS "C5'" "C4'" SING N N 14 AGS "C4'" "O4'" SING N N 15 AGS "C4'" "C3'" SING N N 16 AGS "O4'" "C1'" SING N N 17 AGS "C3'" "O3'" SING N N 18 AGS "C3'" "C2'" SING N N 19 AGS "C2'" "O2'" SING N N 20 AGS "C2'" "C1'" SING N N 21 AGS "C1'" N9 SING N N 22 AGS N9 C8 SING Y N 23 AGS N9 C4 SING Y N 24 AGS C8 N7 DOUB Y N 25 AGS N7 C5 SING Y N 26 AGS C5 C6 SING Y N 27 AGS C5 C4 DOUB Y N 28 AGS C6 N6 SING N N 29 AGS C6 N1 DOUB Y N 30 AGS N1 C2 SING Y N 31 AGS C2 N3 DOUB Y N 32 AGS N3 C4 SING Y N 33 AGS O2G HOG2 SING N N 34 AGS O3G H21 SING N N 35 AGS O2B HOB2 SING N N 36 AGS O2A HOA2 SING N N 37 AGS "C5'" "H5'1" SING N N 38 AGS "C5'" "H5'2" SING N N 39 AGS "C4'" "H4'" SING N N 40 AGS "C3'" "H3'" SING N N 41 AGS "O3'" "HO3'" SING N N 42 AGS "C2'" "H2'" SING N N 43 AGS "O2'" "HO2'" SING N N 44 AGS "C1'" "H1'" SING N N 45 AGS C8 H8 SING N N 46 AGS N6 HN61 SING N N 47 AGS N6 HN62 SING N N 48 AGS C2 H2 SING N N 49 # # 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 AGS SMILES ACDLabs 12.01 "O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O" AGS InChI InChI 1.03 "InChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1" AGS InChIKey InChI 1.03 NLTUCYMLOPLUHL-KQYNXXCUSA-N AGS SMILES_CANONICAL CACTVS 3.370 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O" AGS SMILES CACTVS 3.370 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O" AGS SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N" AGS SMILES "OpenEye OEToolkits" 1.7.6 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)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 AGS "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(S)-hydroxy{[(S)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]adenosine" AGS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] bis(oxidanyl)phosphinothioyl 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 AGS "Create component" 1999-07-08 PDBJ AGS "Modify descriptor" 2011-06-04 RCSB AGS "Other modification" 2012-02-03 RCSB AGS "Other modification" 2013-02-04 RCSB AGS "Modify synonyms" 2020-06-05 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 AGS ATP-GAMMA-S ? ? 2 AGS "ADENOSINE 5'-(3-THIOTRIPHOSPHATE)" ? ? 3 AGS "ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE)" ? ? 4 AGS "ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" ? ? ##