data_TDP # _chem_comp.id TDP _chem_comp.name "THIAMIN DIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H18 N4 O7 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2022-02-08 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status OBS _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 424.306 _chem_comp.one_letter_code ? _chem_comp.three_letter_code TDP _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 Y _chem_comp.pdbx_model_coordinates_db_code 1QS0 _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 TDP "N1'" N1* N 0 1 Y N N -6.527 -9.534 108.842 5.793 2.278 0.190 "N1'" TDP 1 TDP "C2'" C2* C 0 1 Y N N -5.186 -9.835 109.042 6.839 1.561 0.548 "C2'" TDP 2 TDP C2A C2A C 0 1 N N N -4.143 -8.756 109.094 7.943 2.218 1.336 C2A TDP 3 TDP "N3'" N3* N 0 1 Y N N -4.778 -11.089 109.196 6.950 0.287 0.230 "N3'" TDP 4 TDP "C4'" C4* C 0 1 Y N N -5.696 -12.135 109.161 5.992 -0.326 -0.460 "C4'" TDP 5 TDP "N4'" N4* N 0 1 N N N -5.188 -13.354 109.324 6.110 -1.667 -0.787 "N4'" TDP 6 TDP "C5'" C5* C 0 1 Y N N -7.100 -11.874 108.959 4.870 0.405 -0.854 "C5'" TDP 7 TDP "C6'" C6* C 0 1 Y N N -7.437 -10.564 108.808 4.800 1.739 -0.503 "C6'" TDP 8 TDP C35 C35 C 0 1 N N N -8.140 -12.988 108.909 3.763 -0.245 -1.643 C35 TDP 9 TDP N3 N3 N 1 1 Y N N -7.978 -13.793 107.609 2.829 -0.901 -0.724 N3 TDP 10 TDP C2 C2 C 0 1 Y N N -7.296 -14.930 107.645 2.988 -2.175 -0.449 C2 TDP 11 TDP S1 S1 S 0 1 Y N N -7.151 -15.728 106.191 1.677 -2.479 0.649 S1 TDP 12 TDP C5 C5 C 0 1 Y N N -8.058 -14.498 105.412 0.995 -0.827 0.657 C5 TDP 13 TDP C4 C4 C 0 1 Y N N -8.438 -13.516 106.319 1.853 -0.199 -0.188 C4 TDP 14 TDP C4A C4A C 0 1 N N N -9.230 -12.313 105.959 1.685 1.263 -0.512 C4A TDP 15 TDP C5A C5A C 0 1 N N N -8.305 -14.615 103.953 -0.197 -0.281 1.399 C5A TDP 16 TDP C5B C5B C 0 1 N N N -7.184 -14.087 103.087 -1.452 -0.442 0.539 C5B TDP 17 TDP O5G O5G O 0 1 N N N -7.287 -14.561 101.784 -2.582 0.076 1.243 O5G TDP 18 TDP P1 P1 P 0 1 N N R -6.295 -14.665 100.552 -3.860 -0.124 0.284 P1 TDP 19 TDP O11 O11 O 0 1 N N N -5.678 -16.066 100.810 -5.151 0.557 0.961 O11 TDP 20 TDP O12 O12 O 0 1 N N N -7.019 -14.626 99.293 -4.131 -1.697 0.073 O12 TDP 21 TDP O13 O13 O 0 1 N N N -5.217 -13.675 100.796 -3.597 0.511 -1.027 O13 TDP 22 TDP P2 P2 P 0 1 N N N -6.266 -17.560 100.783 -6.271 0.678 -0.190 P2 TDP 23 TDP O21 O21 O 0 1 N N N -5.083 -18.460 100.401 -7.702 0.978 0.484 O21 TDP 24 TDP O22 O22 O -1 1 N N N -7.033 -17.729 102.010 -5.901 1.832 -1.148 O22 TDP 25 TDP O23 O23 O 0 1 N N N -7.202 -17.503 99.594 -6.341 -0.647 -0.981 O23 TDP 26 TDP H2A1 1H2A H 0 0 N N N -3.066 -8.997 109.254 7.735 2.122 2.402 H2A1 TDP 27 TDP H2A2 2H2A H 0 0 N N N -4.224 -8.153 108.159 8.892 1.734 1.105 H2A2 TDP 28 TDP H2A3 3H2A H 0 0 N N N -4.449 -8.018 109.871 8.000 3.274 1.071 H2A3 TDP 29 TDP "H4'1" 1H4* H 0 0 N N N -5.860 -14.120 109.298 5.409 -2.105 -1.294 "H4'1" TDP 30 TDP "H4'2" 2H4* H 0 0 N N N -4.648 -13.393 110.188 6.893 -2.167 -0.509 "H4'2" TDP 31 TDP "H6'" H6* H 0 1 N N N -8.502 -10.324 108.650 3.947 2.336 -0.791 "H6'" TDP 32 TDP H351 1H35 H 0 0 N N N -8.100 -13.639 109.813 3.233 0.514 -2.218 H351 TDP 33 TDP H352 2H35 H 0 0 N N N -9.177 -12.599 109.035 4.186 -0.986 -2.321 H352 TDP 34 TDP H2 H2 H 0 1 N N N -6.930 -15.160 108.659 3.740 -2.859 -0.813 H2 TDP 35 TDP H4A1 1H4A H 0 0 N N N -9.597 -12.092 104.929 2.325 1.855 0.142 H4A1 TDP 36 TDP H4A2 2H4A H 0 0 N N N -10.117 -12.291 106.633 1.965 1.439 -1.550 H4A2 TDP 37 TDP H4A3 3H4A H 0 0 N N N -8.646 -11.424 106.295 0.645 1.551 -0.361 H4A3 TDP 38 TDP H5A1 1H5A H 0 0 N N N -8.542 -15.670 103.681 -0.325 -0.828 2.334 H5A1 TDP 39 TDP H5A2 2H5A H 0 0 N N N -9.269 -14.126 103.681 -0.038 0.775 1.616 H5A2 TDP 40 TDP H5B1 1H5B H 0 0 N N N -7.134 -12.973 103.114 -1.324 0.105 -0.395 H5B1 TDP 41 TDP H5B2 2H5B H 0 0 N N N -6.185 -14.313 103.527 -1.611 -1.498 0.322 H5B2 TDP 42 TDP H13 H13 H 0 1 N N N -4.622 -13.737 100.057 ? ? ? H13 TDP 43 TDP H23 H23 H 0 1 N N N -7.549 -18.386 99.578 ? ? ? H23 TDP 44 # # 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 TDP "N1'" "C2'" DOUB Y N 1 TDP "N1'" "C6'" SING Y N 2 TDP "C2'" C2A SING N N 3 TDP "C2'" "N3'" SING Y N 4 TDP C2A H2A1 SING N N 5 TDP C2A H2A2 SING N N 6 TDP C2A H2A3 SING N N 7 TDP "N3'" "C4'" DOUB Y N 8 TDP "C4'" "N4'" SING N N 9 TDP "C4'" "C5'" SING Y N 10 TDP "N4'" "H4'1" SING N N 11 TDP "N4'" "H4'2" SING N N 12 TDP "C5'" "C6'" DOUB Y N 13 TDP "C5'" C35 SING N N 14 TDP "C6'" "H6'" SING N N 15 TDP C35 N3 SING N N 16 TDP C35 H351 SING N N 17 TDP C35 H352 SING N N 18 TDP N3 C2 DOUB Y N 19 TDP N3 C4 SING Y N 20 TDP C2 S1 SING Y N 21 TDP C2 H2 SING N N 22 TDP S1 C5 SING Y N 23 TDP C5 C4 DOUB Y N 24 TDP C5 C5A SING N N 25 TDP C4 C4A SING N N 26 TDP C4A H4A1 SING N N 27 TDP C4A H4A2 SING N N 28 TDP C4A H4A3 SING N N 29 TDP C5A C5B SING N N 30 TDP C5A H5A1 SING N N 31 TDP C5A H5A2 SING N N 32 TDP C5B O5G SING N N 33 TDP C5B H5B1 SING N N 34 TDP C5B H5B2 SING N N 35 TDP O5G P1 SING N N 36 TDP P1 O11 SING N N 37 TDP P1 O12 DOUB N N 38 TDP P1 O13 SING N N 39 TDP O11 P2 SING N N 40 TDP O13 H13 SING N N 41 TDP P2 O21 DOUB N N 42 TDP P2 O22 SING N N 43 TDP P2 O23 SING N N 44 TDP O23 H23 SING N N 45 # # 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 TDP SMILES_CANONICAL CACTVS 3.341 "Cc1ncc(C[n+]2csc(CCO[P@](O)(=O)O[P](O)([O-])=O)c2C)c(N)n1" TDP SMILES CACTVS 3.341 "Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)([O-])=O)c2C)c(N)n1" TDP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@@](=O)(O)O[P@](=O)(O)[O-]" TDP SMILES "OpenEye OEToolkits" 1.5.0 "Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)[O-]" TDP InChI InChI 1.03 "InChI=1S/C12H18N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)" TDP InChIKey InChI 1.03 AYEKOFBPNLCAJY-UHFFFAOYSA-N # _pdbx_chem_comp_identifier.comp_id TDP _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 1.5.0 _pdbx_chem_comp_identifier.identifier "[2-[3-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium-5-yl]ethoxy-hydroxy-phosphoryl] 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 TDP "Create component" 1999-07-08 PDBJ TDP "Modify descriptor" 2011-06-04 RCSB TDP "Obsolete component" 2021-08-10 PDBE TDP "Other modification" 2022-02-08 RCSB ##