data_TOG # _chem_comp.id TOG _chem_comp.name ;4-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3 -ium-2-yl]-4-oxidanyl-butanoic acid ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H24 N4 O10 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "ThDP and decarboxylated 2-oxoglutarate adduct, covalent intermediate I, carboanion form" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-11-17 _chem_comp.pdbx_modified_date 2024-09-25 _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 526.395 _chem_comp.one_letter_code ? _chem_comp.three_letter_code TOG _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 5ESS _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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 TOG O21 O1 O 0 1 N N N N N N -23.991 13.031 -17.567 ? ? ? O21 TOG 1 TOG P2 P1 P 0 1 N N N N N N -24.688 12.330 -18.719 ? ? ? P2 TOG 2 TOG O22 O2 O 0 1 N N N N N N -23.827 11.982 -19.908 ? ? ? O22 TOG 3 TOG O23 O3 O 0 1 N N N N N N -25.947 13.069 -19.111 ? ? ? O23 TOG 4 TOG O11 O4 O 0 1 N N N N N N -25.097 10.832 -18.217 ? ? ? O11 TOG 5 TOG P1 P2 P 0 1 N N N N N N -25.150 10.310 -16.683 ? ? ? P1 TOG 6 TOG O12 O5 O 0 1 N N N N N N -25.380 8.820 -16.737 ? ? ? O12 TOG 7 TOG O13 O6 O 0 1 N N N N N N -23.956 10.761 -15.885 ? ? ? O13 TOG 8 TOG O5G O7 O 0 1 N N N N N N -26.433 11.037 -16.044 ? ? ? O5G TOG 9 TOG C5B C1 C 0 1 N N N N N N -27.776 10.595 -16.307 ? ? ? C5B TOG 10 TOG C5A C2 C 0 1 N N N N N N -28.741 11.628 -15.733 ? ? ? C5A TOG 11 TOG C5 C3 C 0 1 Y N N N N N -30.202 11.340 -16.025 ? ? ? C5 TOG 12 TOG S1 S1 S 0 1 Y N N N N N -30.702 11.380 -17.668 ? ? ? S1 TOG 13 TOG C2 C4 C 0 1 Y N N N N N -32.326 11.007 -17.132 ? ? ? C2 TOG 14 TOG C4 C5 C 0 1 Y N N N N N -31.279 11.079 -15.115 ? ? ? C4 TOG 15 TOG C4A C6 C 0 1 N N N N N N -31.069 11.009 -13.632 ? ? ? C4A TOG 16 TOG N3 N1 N 1 1 Y N N N N N -32.486 10.905 -15.793 ? ? ? N3 TOG 17 TOG C35 C7 C 0 1 N N N N N N -33.760 10.600 -15.153 ? ? ? C35 TOG 18 TOG "C5'" C8 C 0 1 Y N N N N N -33.806 9.137 -14.757 ? ? ? "C5'" TOG 19 TOG "C6'" C9 C 0 1 Y N N N N N -33.845 8.794 -13.428 ? ? ? "C6'" TOG 20 TOG "N1'" N2 N 0 1 Y N N N N N -33.885 7.509 -13.074 ? ? ? "N1'" TOG 21 TOG "C4'" C10 C 0 1 Y N N N N N -33.794 8.030 -15.734 ? ? ? "C4'" TOG 22 TOG "N4'" N3 N 0 1 N N N N N N -33.761 8.260 -17.063 ? ? ? "N4'" TOG 23 TOG "N3'" N4 N 0 1 Y N N N N N -33.834 6.761 -15.289 ? ? ? "N3'" TOG 24 TOG "C2'" C11 C 0 1 Y N N N N N -33.879 6.511 -13.968 ? ? ? "C2'" TOG 25 TOG C2A C12 C 0 1 N N N N N N -33.918 5.094 -13.471 ? ? ? C2A TOG 26 TOG O4 O8 O 0 1 N N N N N N -34.481 10.343 -22.873 ? ? ? O4 TOG 27 TOG C51 C13 C 0 1 N N N N N N -33.658 10.191 -21.942 ? ? ? C51 TOG 28 TOG O3 O9 O 0 1 N N N N N N -32.530 9.667 -22.126 ? ? ? O3 TOG 29 TOG C41 C14 C 0 1 N N N N N N -34.084 10.654 -20.560 ? ? ? C41 TOG 30 TOG C3 C15 C 0 1 N N N N N N -32.922 10.669 -19.572 ? ? ? C3 TOG 31 TOG C21 C16 C -1 1 N N N N N N -33.388 11.090 -18.194 ? ? ? C21 TOG 32 TOG O5 O10 O 0 1 N N N N N N -33.540 12.410 -18.212 ? ? ? O5 TOG 33 TOG H1 H1 H 0 1 N N N N N N -23.073 13.151 -17.778 ? ? ? H1 TOG 34 TOG H2 H2 H 0 1 N N N N N N -25.968 13.182 -20.054 ? ? ? H2 TOG 35 TOG H3 H3 H 0 1 N N N N N N -23.512 10.003 -15.523 ? ? ? H3 TOG 36 TOG H4 H4 H 0 1 N N N N N N -27.932 10.503 -17.392 ? ? ? H4 TOG 37 TOG H5 H5 H 0 1 N N N N N N -27.947 9.620 -15.828 ? ? ? H5 TOG 38 TOG H6 H6 H 0 1 N N N N N N -28.606 11.658 -14.642 ? ? ? H6 TOG 39 TOG H7 H7 H 0 1 N N N N N N -28.490 12.610 -16.160 ? ? ? H7 TOG 40 TOG H8 H8 H 0 1 N N N N N N -31.204 12.009 -13.194 ? ? ? H8 TOG 41 TOG H9 H9 H 0 1 N N N N N N -31.799 10.315 -13.191 ? ? ? H9 TOG 42 TOG H10 H10 H 0 1 N N N N N N -30.050 10.651 -13.423 ? ? ? H10 TOG 43 TOG H11 H11 H 0 1 N N N N N N -33.875 11.224 -14.254 ? ? ? H11 TOG 44 TOG H12 H12 H 0 1 N N N N N N -34.580 10.813 -15.855 ? ? ? H12 TOG 45 TOG H13 H13 H 0 1 N N N N N N -33.843 9.564 -12.671 ? ? ? H13 TOG 46 TOG H14 H14 H 0 1 N N N N N N -33.772 7.388 -17.553 ? ? ? H14 TOG 47 TOG H15 H15 H 0 1 N N N N N N -34.559 8.801 -17.327 ? ? ? H15 TOG 48 TOG H16 H16 H 0 1 N N N N N N -33.903 4.404 -14.327 ? ? ? H16 TOG 49 TOG H17 H17 H 0 1 N N N N N N -33.042 4.905 -12.833 ? ? ? H17 TOG 50 TOG H18 H18 H 0 1 N N N N N N -34.837 4.935 -12.888 ? ? ? H18 TOG 51 TOG H19 H19 H 0 1 N N N N N N -32.436 9.429 -23.041 ? ? ? H19 TOG 52 TOG H20 H20 H 0 1 N N N N N N -34.495 11.671 -20.639 ? ? ? H20 TOG 53 TOG H21 H21 H 0 1 N N N N N N -34.861 9.973 -20.182 ? ? ? H21 TOG 54 TOG H22 H22 H 0 1 N N N N N N -32.487 9.660 -19.512 ? ? ? H22 TOG 55 TOG H23 H23 H 0 1 N N N N N N -32.158 11.377 -19.926 ? ? ? H23 TOG 56 TOG H25 H25 H 0 1 N N N N N N -33.833 12.707 -17.359 ? ? ? H25 TOG 57 # 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 TOG O4 C51 DOUB N N 1 TOG O3 C51 SING N N 2 TOG C51 C41 SING N N 3 TOG C41 C3 SING N N 4 TOG O22 P2 DOUB N N 5 TOG C3 C21 SING N N 6 TOG O23 P2 SING N N 7 TOG P2 O11 SING N N 8 TOG P2 O21 SING N N 9 TOG O11 P1 SING N N 10 TOG O5 C21 SING N N 11 TOG C21 C2 SING N N 12 TOG S1 C2 SING Y N 13 TOG S1 C5 SING Y N 14 TOG C2 N3 DOUB Y N 15 TOG "N4'" "C4'" SING N N 16 TOG O12 P1 DOUB N N 17 TOG P1 O5G SING N N 18 TOG P1 O13 SING N N 19 TOG C5B O5G SING N N 20 TOG C5B C5A SING N N 21 TOG C5 C5A SING N N 22 TOG C5 C4 DOUB Y N 23 TOG N3 C35 SING N N 24 TOG N3 C4 SING Y N 25 TOG "C4'" "N3'" DOUB Y N 26 TOG "C4'" "C5'" SING Y N 27 TOG "N3'" "C2'" SING Y N 28 TOG C35 "C5'" SING N N 29 TOG C4 C4A SING N N 30 TOG "C5'" "C6'" DOUB Y N 31 TOG "C2'" C2A SING N N 32 TOG "C2'" "N1'" DOUB Y N 33 TOG "C6'" "N1'" SING Y N 34 TOG O21 H1 SING N N 35 TOG O23 H2 SING N N 36 TOG O13 H3 SING N N 37 TOG C5B H4 SING N N 38 TOG C5B H5 SING N N 39 TOG C5A H6 SING N N 40 TOG C5A H7 SING N N 41 TOG C4A H8 SING N N 42 TOG C4A H9 SING N N 43 TOG C4A H10 SING N N 44 TOG C35 H11 SING N N 45 TOG C35 H12 SING N N 46 TOG "C6'" H13 SING N N 47 TOG "N4'" H14 SING N N 48 TOG "N4'" H15 SING N N 49 TOG C2A H16 SING N N 50 TOG C2A H17 SING N N 51 TOG C2A H18 SING N N 52 TOG O3 H19 SING N N 53 TOG C41 H20 SING N N 54 TOG C41 H21 SING N N 55 TOG C3 H22 SING N N 56 TOG C3 H23 SING N N 57 TOG O5 H25 SING N N 58 # 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 TOG InChI InChI 1.03 "InChI=1S/C16H24N4O10P2S/c1-9-13(5-6-29-32(27,28)30-31(24,25)26)33-16(12(21)3-4-14(22)23)20(9)8-11-7-18-10(2)19-15(11)17/h7,21H,3-6,8H2,1-2H3,(H,22,23)(H,27,28)(H2,17,18,19)(H2,24,25,26)" TOG InChIKey InChI 1.03 VGWJMSNWDAXPBE-UHFFFAOYSA-N TOG SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C-](O)CCC(O)=O)c(N)n1" TOG SMILES CACTVS 3.385 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C-](O)CCC(O)=O)c(N)n1" TOG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C-](CCC(=O)O)O)CCOP(=O)(O)OP(=O)(O)O" TOG SMILES "OpenEye OEToolkits" 2.0.4 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C-](CCC(=O)O)O)CCOP(=O)(O)OP(=O)(O)O" # _pdbx_chem_comp_identifier.comp_id TOG _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.4 _pdbx_chem_comp_identifier.identifier "4-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-4-oxidanyl-butanoic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site TOG "Create component" 2015-11-17 RCSB TOG "Initial release" 2016-06-22 RCSB TOG "Modify synonyms" 2020-06-05 PDBE TOG "Other modification" 2024-09-25 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id TOG _pdbx_chem_comp_synonyms.name "ThDP and decarboxylated 2-oxoglutarate adduct, covalent intermediate I, carboanion form" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? #