data_TOI # _chem_comp.id TOI _chem_comp.name ;(1~{R},2~{S},5~{S},6~{S})-2-[(1~{S})-1-[3-[(4-azanylidene-2-methyl-1~{H}-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl (phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-1,4-bis(oxidanyl)-4-oxidanylidene-butyl]-6-oxidanyl-5-(3-oxid anyl-3-oxidanylidene-prop-1-en-2-yl)oxy-cyclohex-3-ene-1-carboxylic acid ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C26 H35 N4 O16 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "ThDP, decarboxylated 2-oxoglutarate and isochorismate adduct, covalent intermediate II" _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2015-11-17 _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 ? _chem_comp.formula_weight 753.586 _chem_comp.one_letter_code ? _chem_comp.three_letter_code TOI _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 5ESU _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 TOI O2P O1 O 0 1 N N N -67.828 15.677 28.208 -4.545 -7.686 0.165 O2P TOI 1 TOI C1P C1 C 0 1 N N N -67.496 15.569 27.008 -4.537 -6.594 -0.625 C1P TOI 2 TOI O1P O2 O 0 1 N N N -66.696 16.365 26.469 -4.689 -6.711 -1.825 O1P TOI 3 TOI C2P C2 C 0 1 N N N -68.063 14.459 26.180 -4.344 -5.258 -0.034 C2P TOI 4 TOI C3P C3 C 0 1 N N N -68.912 13.595 26.708 -4.177 -5.129 1.284 C3P TOI 5 TOI O3P O3 O 0 1 N N N -67.659 14.362 24.784 -4.336 -4.156 -0.831 O3P TOI 6 TOI C5I C4 C 0 1 N N S -68.019 13.148 24.128 -4.191 -2.889 -0.185 C5I TOI 7 TOI C6I C5 C 0 1 N N S -66.889 12.814 23.171 -4.799 -1.798 -1.069 C6I TOI 8 TOI O3I O4 O 0 1 N N N -65.731 12.436 23.928 -6.222 -1.924 -1.079 O3I TOI 9 TOI C1I C6 C 0 1 N N R -67.202 11.711 22.156 -4.406 -0.432 -0.491 C1I TOI 10 TOI CI C7 C 0 1 N N N -66.347 12.013 20.950 -5.135 0.660 -1.231 CI TOI 11 TOI O2I O5 O 0 1 N N N -65.201 12.477 21.139 -6.346 1.061 -0.813 O2I TOI 12 TOI O1I O6 O 0 1 N N N -66.790 11.799 19.804 -4.630 1.173 -2.201 O1I TOI 13 TOI C4I C8 C 0 1 N N N -69.253 13.371 23.301 -2.734 -2.612 0.045 C4I TOI 14 TOI C3I C9 C 0 1 N N N -69.651 12.422 22.461 -2.174 -1.463 -0.156 C3I TOI 15 TOI C2I C10 C 0 1 N N S -68.677 11.506 21.746 -2.896 -0.252 -0.657 C2I TOI 16 TOI C21 C11 C 0 1 N N S -69.113 10.043 21.951 -2.441 0.976 0.135 C21 TOI 17 TOI C3 C12 C 0 1 N N N -69.546 9.801 23.400 -2.715 0.752 1.624 C3 TOI 18 TOI C41 C13 C 0 1 N N N -69.180 8.396 23.884 -1.665 -0.201 2.198 C41 TOI 19 TOI C51 C14 C 0 1 N N N -69.245 8.278 25.397 -1.848 -0.311 3.690 C51 TOI 20 TOI O3 O7 O 0 1 N N N -70.184 7.634 25.917 -2.784 0.234 4.225 O3 TOI 21 TOI O4 O8 O 0 1 N N N -68.350 8.819 26.083 -0.971 -1.014 4.424 O4 TOI 22 TOI O5 O9 O 0 1 N N N -67.970 9.224 21.707 -3.161 2.126 -0.313 O5 TOI 23 TOI C2 C15 C 0 1 Y N N -70.240 9.665 21.010 -0.965 1.192 -0.077 C2 TOI 24 TOI S1 S1 S 0 1 Y N N -71.861 9.932 21.525 0.022 0.258 -1.114 S1 TOI 25 TOI N3 N1 N 1 1 Y N N -70.229 9.575 19.631 -0.265 2.114 0.493 N3 TOI 26 TOI C35 C16 C 0 1 N N N -69.011 9.349 18.844 -0.868 3.059 1.436 C35 TOI 27 TOI "C5'" C17 C 0 1 N N N -68.897 7.931 18.314 -1.536 4.173 0.672 "C5'" TOI 28 TOI "C4'" C18 C 0 1 N N N -68.778 6.746 19.203 -0.763 5.310 0.151 "C4'" TOI 29 TOI "N4'" N2 N 0 1 N N N -68.784 6.862 20.550 0.473 5.530 0.556 "N4'" TOI 30 TOI "N3'" N3 N 0 1 N N N -68.672 5.526 18.643 -1.356 6.129 -0.759 "N3'" TOI 31 TOI "C2'" C19 C 0 1 N N N -68.663 5.386 17.299 -2.645 6.066 -0.951 "C2'" TOI 32 TOI C2A C20 C 0 1 N N N -68.540 4.004 16.711 -3.283 6.976 -1.968 C2A TOI 33 TOI "N1'" N4 N 0 1 N N N -68.762 6.447 16.485 -3.422 5.201 -0.257 "N1'" TOI 34 TOI "C6'" C21 C 0 1 N N N -68.872 7.700 16.946 -2.866 4.159 0.435 "C6'" TOI 35 TOI C4 C22 C 0 1 Y N N -71.481 9.736 18.994 1.017 2.167 0.191 C4 TOI 36 TOI C4A C23 C 0 1 N N N -71.713 9.689 17.505 1.952 3.191 0.783 C4A TOI 37 TOI C5 C24 C 0 1 Y N N -72.466 9.929 19.899 1.421 1.235 -0.677 C5 TOI 38 TOI C5A C25 C 0 1 N N N -73.927 10.145 19.551 2.824 1.059 -1.199 C5A TOI 39 TOI C5B C26 C 0 1 N N N -74.833 9.075 20.155 3.594 0.107 -0.280 C5B TOI 40 TOI O5G O10 O 0 1 N N N -76.195 9.352 19.817 4.924 -0.060 -0.775 O5G TOI 41 TOI P1 P1 P 0 1 N N N -77.415 8.479 20.417 6.016 -0.998 -0.054 P1 TOI 42 TOI O13 O11 O 0 1 N N N -78.681 8.879 19.699 6.162 -0.587 1.360 O13 TOI 43 TOI O12 O12 O 0 1 N N N -76.998 7.028 20.382 5.534 -2.532 -0.120 O12 TOI 44 TOI O11 O13 O 0 1 N N N -77.507 8.916 21.970 7.432 -0.847 -0.805 O11 TOI 45 TOI P2 P2 P 0 1 N N N -78.042 10.338 22.524 8.946 -1.244 -0.428 P2 TOI 46 TOI O23 O14 O 0 1 N N N -76.797 11.093 22.922 9.517 -0.207 0.664 O23 TOI 47 TOI O21 O15 O 0 1 N N N -78.801 10.986 21.390 8.972 -2.614 0.133 O21 TOI 48 TOI O22 O16 O 0 1 N N N -78.904 9.931 23.694 9.861 -1.189 -1.751 O22 TOI 49 TOI H1 H1 H 0 1 N N N -67.386 16.424 28.593 -4.675 -8.540 -0.268 H1 TOI 50 TOI H2 H2 H 0 1 N N N -69.202 13.687 27.744 -3.931 -4.166 1.705 H2 TOI 51 TOI H3 H3 H 0 1 N N N -69.316 12.797 26.103 -4.287 -5.989 1.928 H3 TOI 52 TOI H4 H4 H 0 1 N N N -68.173 12.326 24.843 -4.711 -2.910 0.772 H4 TOI 53 TOI H5 H5 H 0 1 N N N -66.655 13.726 22.603 -4.415 -1.893 -2.085 H5 TOI 54 TOI H6 H6 H 0 1 N N N -65.530 13.116 24.561 -6.539 -2.773 -1.418 H6 TOI 55 TOI H7 H7 H 0 1 N N N -66.849 10.761 22.585 -4.666 -0.394 0.567 H7 TOI 56 TOI H8 H8 H 0 1 N N N -64.775 12.620 20.302 -6.775 1.764 -1.320 H8 TOI 57 TOI H9 H9 H 0 1 N N N -69.810 14.292 23.388 -2.115 -3.422 0.403 H9 TOI 58 TOI H11 H11 H 0 1 N N N -70.709 12.298 22.280 -1.117 -1.372 0.050 H11 TOI 59 TOI H13 H13 H 0 1 N N N -68.749 11.721 20.670 -2.663 -0.107 -1.712 H13 TOI 60 TOI H14 H14 H 0 1 N N N -69.049 10.539 24.047 -2.667 1.705 2.150 H14 TOI 61 TOI H15 H15 H 0 1 N N N -70.636 9.927 23.470 -3.707 0.317 1.750 H15 TOI 62 TOI H16 H16 H 0 1 N N N -69.882 7.674 23.441 -1.780 -1.185 1.744 H16 TOI 63 TOI H17 H17 H 0 1 N N N -68.157 8.162 23.554 -0.668 0.184 1.982 H17 TOI 64 TOI H18 H18 H 0 1 N N N -68.514 8.655 27.004 -1.130 -1.056 5.377 H18 TOI 65 TOI H19 H19 H 0 1 N N N -67.271 9.470 22.302 -2.966 2.381 -1.226 H19 TOI 66 TOI H20 H20 H 0 1 N N N -68.139 9.555 19.482 -1.608 2.542 2.046 H20 TOI 67 TOI H21 H21 H 0 1 N N N -69.013 10.042 17.990 -0.093 3.475 2.080 H21 TOI 68 TOI H22 H22 H 0 1 N N N -68.704 5.974 21.003 0.946 6.324 0.261 H22 TOI 69 TOI H24 H24 H 0 1 N N N -68.471 3.265 17.522 -2.517 7.600 -2.429 H24 TOI 70 TOI H25 H25 H 0 1 N N N -69.424 3.789 16.093 -3.773 6.376 -2.736 H25 TOI 71 TOI H26 H26 H 0 1 N N N -67.635 3.950 16.088 -4.021 7.610 -1.477 H26 TOI 72 TOI H27 H27 H 0 1 N N N -68.941 8.527 16.255 -3.480 3.346 0.794 H27 TOI 73 TOI H28 H28 H 0 1 N N N -71.924 8.654 17.199 2.521 2.737 1.594 H28 TOI 74 TOI H29 H29 H 0 1 N N N -72.569 10.330 17.247 2.636 3.546 0.012 H29 TOI 75 TOI H30 H30 H 0 1 N N N -70.815 10.050 16.983 1.374 4.030 1.170 H30 TOI 76 TOI H31 H31 H 0 1 N N N -74.239 11.129 19.932 2.787 0.642 -2.205 H31 TOI 77 TOI H32 H32 H 0 1 N N N -74.036 10.124 18.457 3.327 2.025 -1.224 H32 TOI 78 TOI H33 H33 H 0 1 N N N -74.550 8.089 19.757 3.630 0.524 0.726 H33 TOI 79 TOI H34 H34 H 0 1 N N N -74.720 9.075 21.249 3.091 -0.860 -0.255 H34 TOI 80 TOI H35 H35 H 0 1 N N N -77.631 6.528 19.879 5.418 -2.869 -1.019 H35 TOI 81 TOI H36 H36 H 0 1 N N N -76.706 11.865 22.375 9.530 0.712 0.364 H36 TOI 82 TOI H37 H37 H 0 1 N N N -79.809 10.158 23.515 10.788 -1.417 -1.598 H37 TOI 83 TOI H10 H10 H 0 1 N N N -68.753 6.297 15.496 -4.385 5.316 -0.257 H10 TOI 84 # # 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 TOI "N1'" "C6'" SING N N 1 TOI "N1'" "C2'" SING N N 2 TOI C2A "C2'" SING N N 3 TOI "C6'" "C5'" DOUB N N 4 TOI "C2'" "N3'" DOUB N N 5 TOI C4A C4 SING N N 6 TOI "C5'" C35 SING N N 7 TOI "C5'" "C4'" SING N N 8 TOI "N3'" "C4'" SING N N 9 TOI C35 N3 SING N N 10 TOI C4 N3 SING Y N 11 TOI C4 C5 DOUB Y N 12 TOI "C4'" "N4'" DOUB N N 13 TOI C5A C5 SING N N 14 TOI C5A C5B SING N N 15 TOI N3 C2 DOUB Y N 16 TOI O13 P1 DOUB N N 17 TOI O1I CI DOUB N N 18 TOI O5G C5B SING N N 19 TOI O5G P1 SING N N 20 TOI C5 S1 SING Y N 21 TOI O12 P1 SING N N 22 TOI P1 O11 SING N N 23 TOI CI O2I SING N N 24 TOI CI C1I SING N N 25 TOI C2 S1 SING Y N 26 TOI C2 C21 SING N N 27 TOI O21 P2 DOUB N N 28 TOI O5 C21 SING N N 29 TOI C2I C21 SING N N 30 TOI C2I C1I SING N N 31 TOI C2I C3I SING N N 32 TOI C21 C3 SING N N 33 TOI O11 P2 SING N N 34 TOI C1I C6I SING N N 35 TOI C3I C4I DOUB N N 36 TOI P2 O23 SING N N 37 TOI P2 O22 SING N N 38 TOI C6I O3I SING N N 39 TOI C6I C5I SING N N 40 TOI C4I C5I SING N N 41 TOI C3 C41 SING N N 42 TOI C41 C51 SING N N 43 TOI C5I O3P SING N N 44 TOI O3P C2P SING N N 45 TOI C51 O3 DOUB N N 46 TOI C51 O4 SING N N 47 TOI C2P C3P DOUB N N 48 TOI C2P C1P SING N N 49 TOI O1P C1P DOUB N N 50 TOI C1P O2P SING N N 51 TOI O2P H1 SING N N 52 TOI C3P H2 SING N N 53 TOI C3P H3 SING N N 54 TOI C5I H4 SING N N 55 TOI C6I H5 SING N N 56 TOI O3I H6 SING N N 57 TOI C1I H7 SING N N 58 TOI O2I H8 SING N N 59 TOI C4I H9 SING N N 60 TOI C3I H11 SING N N 61 TOI C2I H13 SING N N 62 TOI C3 H14 SING N N 63 TOI C3 H15 SING N N 64 TOI C41 H16 SING N N 65 TOI C41 H17 SING N N 66 TOI O4 H18 SING N N 67 TOI O5 H19 SING N N 68 TOI C35 H20 SING N N 69 TOI C35 H21 SING N N 70 TOI "N4'" H22 SING N N 71 TOI C2A H24 SING N N 72 TOI C2A H25 SING N N 73 TOI C2A H26 SING N N 74 TOI "C6'" H27 SING N N 75 TOI C4A H28 SING N N 76 TOI C4A H29 SING N N 77 TOI C4A H30 SING N N 78 TOI C5A H31 SING N N 79 TOI C5A H32 SING N N 80 TOI C5B H33 SING N N 81 TOI C5B H34 SING N N 82 TOI O12 H35 SING N N 83 TOI O23 H36 SING N N 84 TOI O22 H37 SING N N 85 TOI "N1'" H10 SING N N 86 # # 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 TOI InChI InChI 1.03 "InChI=1S/C26H34N4O16P2S/c1-12-18(7-9-44-48(42,43)46-47(39,40)41)49-25(30(12)11-15-10-28-14(3)29-22(15)27)26(38,8-6-19(31)32)16-4-5-17(45-13(2)23(34)35)21(33)20(16)24(36)37/h4-5,10,16-17,20-21,33,38H,2,6-9,11H2,1,3H3,(H7-,27,28,29,31,32,34,35,36,37,39,40,41,42,43)/p+1/t16-,17-,20+,21+,26-/m0/s1" TOI InChIKey InChI 1.03 AJVZCJMDQDMTBE-BLORIJLWSA-O TOI SMILES_CANONICAL CACTVS 3.385 "CC1=NC(=N)C(=CN1)C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C@](O)(CCC(O)=O)[C@H]3C=C[C@H](OC(=C)C(O)=O)[C@@H](O)[C@@H]3C(O)=O" TOI SMILES CACTVS 3.385 "CC1=NC(=N)C(=CN1)C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C](O)(CCC(O)=O)[CH]3C=C[CH](OC(=C)C(O)=O)[CH](O)[CH]3C(O)=O" TOI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "[H]/N=C/1\C(=CNC(=N1)C)C[n+]2c(c(sc2[C@](CCC(=O)O)([C@H]3C=C[C@@H]([C@H]([C@@H]3C(=O)O)O)OC(=C)C(=O)O)O)CCOP(=O)(O)OP(=O)(O)O)C" TOI SMILES "OpenEye OEToolkits" 2.0.4 "Cc1c(sc([n+]1CC2=CNC(=NC2=N)C)C(CCC(=O)O)(C3C=CC(C(C3C(=O)O)O)OC(=C)C(=O)O)O)CCOP(=O)(O)OP(=O)(O)O" # _pdbx_chem_comp_identifier.comp_id TOI _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 "(1~{R},2~{S},5~{S},6~{S})-2-[(1~{S})-1-[3-[(4-azanylidene-2-methyl-1~{H}-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-1,4-bis(oxidanyl)-4-oxidanylidene-butyl]-6-oxidanyl-5-(3-oxidanyl-3-oxidanylidene-prop-1-en-2-yl)oxy-cyclohex-3-ene-1-carboxylic 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 TOI "Create component" 2015-11-17 RCSB TOI "Initial release" 2016-06-22 RCSB TOI "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id TOI _pdbx_chem_comp_synonyms.name "ThDP, decarboxylated 2-oxoglutarate and isochorismate adduct, covalent intermediate II" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##