data_THD # _chem_comp.id THD _chem_comp.name ;2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-2-(1,2-DIHYDROXYETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H22 N4 O9 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "({ALPHA,BETA}-DIHYDROXYETHYL)-THIAMIN DIPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-11-09 _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 484.358 _chem_comp.one_letter_code ? _chem_comp.three_letter_code THD _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 N _chem_comp.pdbx_model_coordinates_db_code 1GPU _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 THD "N1'" "N1'" N 0 1 Y N N -3.041 61.454 19.848 1.428 1.481 5.541 "N1'" THD 1 THD "C2'" "C2'" C 0 1 Y N N -2.184 60.470 20.188 2.050 0.833 6.505 "C2'" THD 2 THD CM2 CM2 C 0 1 N N N -0.873 60.838 20.682 2.653 1.615 7.643 CM2 THD 3 THD "N3'" "N3'" N 0 1 Y N N -2.532 59.196 20.071 2.164 -0.479 6.498 "N3'" THD 4 THD "C4'" "C4'" C 0 1 Y N N -3.803 58.840 19.598 1.639 -1.201 5.512 "C4'" THD 5 THD "N4'" "N4'" N 0 1 N N N -4.019 57.528 19.535 1.757 -2.581 5.511 "N4'" THD 6 THD "C5'" "C5'" C 0 1 Y N N -4.775 59.864 19.219 0.974 -0.545 4.475 "C5'" THD 7 THD "C6'" "C6'" C 0 1 Y N N -4.314 61.147 19.373 0.884 0.832 4.522 "C6'" THD 8 THD "C7'" "C7'" C 0 1 N N N -6.195 59.594 18.689 0.369 -1.320 3.333 "C7'" THD 9 THD N3 N3 N 0 1 N N N -6.112 58.680 17.427 -0.262 -0.391 2.393 N3 THD 10 THD C2 C2 C 0 1 N N N -6.228 57.285 17.358 -1.577 0.052 2.586 C2 THD 11 THD S1 S1 S 0 1 N N N -5.973 56.722 15.756 -1.793 1.127 1.176 S1 THD 12 THD C5 C5 C 0 1 N N N -5.752 58.299 15.189 -0.178 0.909 0.448 C5 THD 13 THD C4 C4 C 0 1 N N N -5.856 59.211 16.208 0.409 0.067 1.292 C4 THD 14 THD CM4 CM4 C 0 1 N N N -5.708 60.684 16.020 1.823 -0.385 1.035 CM4 THD 15 THD C6 C6 C 0 1 N N N -5.468 58.595 13.730 0.379 1.526 -0.809 C6 THD 16 THD C7 C7 C 0 1 N N N -5.621 57.464 12.801 0.070 0.619 -2.002 C7 THD 17 THD O7 O7 O 0 1 N N N -4.798 57.778 11.677 0.598 1.203 -3.194 O7 THD 18 THD PA PA P 0 1 N N R -3.699 56.763 11.303 0.239 0.202 -4.402 PA THD 19 THD O1A O1A O 0 1 N N N -2.538 56.617 12.250 -1.358 0.038 -4.506 O1A THD 20 THD O2A O2A O 0 1 N N N -3.433 57.289 9.996 0.855 -1.119 -4.147 O2A THD 21 THD O3A O3A O 0 1 N N N -4.402 55.393 10.820 0.808 0.801 -5.783 O3A THD 22 THD PB PB P 0 1 N N N -5.639 54.735 10.025 0.415 -0.244 -6.942 PB THD 23 THD O1B O1B O 0 1 N N N -4.978 54.712 8.730 -1.056 -0.388 -6.998 O1B THD 24 THD O2B O2B O 0 1 N N N -5.798 53.395 10.573 0.957 0.294 -8.359 O2B THD 25 THD O3B O3B O 0 1 N N N -6.849 55.575 10.209 1.082 -1.674 -6.622 O3B THD 26 THD C8 C8 C 0 1 N N N -6.621 56.702 18.419 -2.436 -0.242 3.566 C8 THD 27 THD O9 O9 O 0 1 N N N -6.947 57.126 19.553 -2.030 -1.006 4.622 O9 THD 28 THD C9 C9 C 0 1 N N N -6.659 55.276 18.152 -3.852 0.268 3.505 C9 THD 29 THD O10 O10 O 0 1 N N N -5.679 54.612 18.927 -4.757 -0.837 3.499 O10 THD 30 THD HM21 1HM2 H 0 0 N N N -0.164 60.024 20.963 1.915 1.728 8.438 HM21 THD 31 THD HM22 2HM2 H 0 0 N N N -0.993 61.530 21.548 3.523 1.083 8.029 HM22 THD 32 THD HM23 3HM2 H 0 0 N N N -0.380 61.508 19.939 2.957 2.599 7.287 HM23 THD 33 THD "H4'1" "1H4'" H 0 0 N N N -5.019 57.248 19.163 2.221 -3.029 6.236 "H4'1" THD 34 THD "H4'2" "2H4'" H 0 0 N N N -3.286 56.755 19.821 1.375 -3.100 4.786 "H4'2" THD 35 THD "H6'" "H6'" H 0 1 N N N -4.987 61.979 19.107 0.376 1.373 3.737 "H6'" THD 36 THD "H7'1" "1H7'" H 0 0 N N N -6.758 60.536 18.491 1.150 -1.881 2.821 "H7'1" THD 37 THD "H7'2" "2H7'" H 0 0 N N N -6.865 59.170 19.473 -0.379 -2.011 3.720 "H7'2" THD 38 THD HM41 1HM4 H 0 0 N N N -5.497 61.121 15.016 2.193 0.079 0.121 HM41 THD 39 THD HM42 2HM4 H 0 0 N N N -4.922 61.044 16.724 2.456 -0.092 1.873 HM42 THD 40 THD HM43 3HM4 H 0 0 N N N -6.623 61.176 16.425 1.844 -1.469 0.926 HM43 THD 41 THD H6C1 1H6C H 0 0 N N N -4.450 59.036 13.625 -0.077 2.503 -0.967 H6C1 THD 42 THD H6C2 2H6C H 0 0 N N N -6.094 59.452 13.389 1.458 1.640 -0.709 H6C2 THD 43 THD H7C1 1H7C H 0 0 N N N -6.681 57.245 12.533 0.526 -0.357 -1.843 H7C1 THD 44 THD H7C2 2H7C H 0 0 N N N -5.394 56.473 13.260 -1.009 0.504 -2.101 H7C2 THD 45 THD HO1A HO1A H 0 0 N N N -1.861 55.992 12.020 -1.719 0.919 -4.672 HO1A THD 46 THD HO2B HO2B H 0 0 N N N -6.527 53.007 10.104 0.701 -0.359 -9.023 HO2B THD 47 THD HO3B HO3B H 0 0 N N N -7.578 55.187 9.740 2.039 -1.537 -6.594 HO3B THD 48 THD H9 H9 H 0 1 N N N -7.240 56.691 20.345 -2.075 -0.443 5.407 H9 THD 49 THD H9C1 1H9C H 0 0 N N N -6.555 55.051 17.065 -4.050 0.894 4.375 H9C1 THD 50 THD H9C2 2H9C H 0 0 N N N -7.677 54.848 18.310 -3.989 0.854 2.596 H9C2 THD 51 THD H10 H10 H 0 1 N N N -5.704 53.679 18.752 -5.650 -0.468 3.460 H10 THD 52 # # 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 THD "N1'" "C2'" DOUB Y N 1 THD "N1'" "C6'" SING Y N 2 THD "C2'" CM2 SING N N 3 THD "C2'" "N3'" SING Y N 4 THD CM2 HM21 SING N N 5 THD CM2 HM22 SING N N 6 THD CM2 HM23 SING N N 7 THD "N3'" "C4'" DOUB Y N 8 THD "C4'" "N4'" SING N N 9 THD "C4'" "C5'" SING Y N 10 THD "N4'" "H4'1" SING N N 11 THD "N4'" "H4'2" SING N N 12 THD "C5'" "C6'" DOUB Y N 13 THD "C5'" "C7'" SING N N 14 THD "C6'" "H6'" SING N N 15 THD "C7'" N3 SING N N 16 THD "C7'" "H7'1" SING N N 17 THD "C7'" "H7'2" SING N N 18 THD N3 C2 SING N N 19 THD N3 C4 SING N N 20 THD C2 S1 SING N N 21 THD C2 C8 DOUB N E 22 THD S1 C5 SING N N 23 THD C5 C4 DOUB N N 24 THD C5 C6 SING N N 25 THD C4 CM4 SING N N 26 THD CM4 HM41 SING N N 27 THD CM4 HM42 SING N N 28 THD CM4 HM43 SING N N 29 THD C6 C7 SING N N 30 THD C6 H6C1 SING N N 31 THD C6 H6C2 SING N N 32 THD C7 O7 SING N N 33 THD C7 H7C1 SING N N 34 THD C7 H7C2 SING N N 35 THD O7 PA SING N N 36 THD PA O1A SING N N 37 THD PA O2A DOUB N N 38 THD PA O3A SING N N 39 THD O1A HO1A SING N N 40 THD O3A PB SING N N 41 THD PB O1B DOUB N N 42 THD PB O2B SING N N 43 THD PB O3B SING N N 44 THD O2B HO2B SING N N 45 THD O3B HO3B SING N N 46 THD C8 O9 SING N N 47 THD C8 C9 SING N N 48 THD O9 H9 SING N N 49 THD C9 O10 SING N N 50 THD C9 H9C1 SING N N 51 THD C9 H9C2 SING N N 52 THD O10 H10 SING N N 53 # # 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 THD SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCCC=1S\C(=C(\O)CO)N(C=1C)Cc2cnc(nc2N)C" THD SMILES_CANONICAL CACTVS 3.341 "Cc1ncc(CN\2C(=C(CCO[P@](O)(=O)O[P](O)(O)=O)SC\2=C(/O)CO)C)c(N)n1" THD SMILES CACTVS 3.341 "Cc1ncc(CN2C(=C(CCO[P](O)(=O)O[P](O)(O)=O)SC2=C(O)CO)C)c(N)n1" THD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1ncc(c(n1)N)CN\2C(=C(S/C2=C(\CO)/O)CCO[P@@](=O)(O)OP(=O)(O)O)C" THD SMILES "OpenEye OEToolkits" 1.5.0 "Cc1ncc(c(n1)N)CN2C(=C(SC2=C(CO)O)CCOP(=O)(O)OP(=O)(O)O)C" THD InChI InChI 1.03 "InChI=1S/C14H22N4O9P2S/c1-8-12(3-4-26-29(24,25)27-28(21,22)23)30-14(11(20)7-19)18(8)6-10-5-16-9(2)17-13(10)15/h5,19-20H,3-4,6-7H2,1-2H3,(H,24,25)(H2,15,16,17)(H2,21,22,23)/b14-11+" THD InChIKey InChI 1.03 LXZUEFPJZTWGEL-SDNWHVSQSA-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 THD "SYSTEMATIC NAME" ACDLabs 10.04 "2-[(2E)-3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-(1,2-dihydroxyethylidene)-4-methyl-2,3-dihydro-1,3-thiazol-5-yl]ethyl trihydrogen diphosphate" THD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "2-[(2E)-3-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-2-(1,2-dihydroxyethylidene)-4-methyl-1,3-thiazol-5-yl]ethyl phosphono 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 THD "Create component" 2001-11-09 EBI THD "Modify descriptor" 2011-06-04 RCSB THD "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id THD _pdbx_chem_comp_synonyms.name "({ALPHA,BETA}-DIHYDROXYETHYL)-THIAMIN DIPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##