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         ? 
# 
