data_TDK # _chem_comp.id TDK _chem_comp.name "3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1S)-1-HYDROXY-1-[(R)-HYDROXY(METHOXY)PHOSPHORYL]ETHYL}-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H26 N4 O11 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2-PHOSPHONOLACTYLTHIAMIN DIPHOSPHATE" _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2005-12-01 _chem_comp.pdbx_modified_date 2021-03-01 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 563.373 _chem_comp.one_letter_code ? _chem_comp.three_letter_code TDK _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 2EZ9 _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 TDK O2B O2B O 0 1 N N N 85.396 59.796 2.252 8.191 1.676 0.642 O2B TDK 1 TDK PB PB P 0 1 N N N 84.512 60.096 1.069 7.984 0.351 -0.249 PB TDK 2 TDK O3B O3B O 0 1 N N N 85.297 60.265 -0.213 8.821 0.488 -1.617 O3B TDK 3 TDK O1B O1B O 0 1 N N N 83.325 59.159 0.940 8.462 -0.830 0.505 O1B TDK 4 TDK O3A O3A O 0 1 N N N 83.944 61.558 1.490 6.421 0.173 -0.591 O3A TDK 5 TDK PA PA P 0 1 N N R 83.807 62.903 0.599 5.138 -0.306 0.256 PA TDK 6 TDK O1A O1A O 0 1 N N N 84.974 63.034 -0.332 5.151 0.348 1.584 O1A TDK 7 TDK O2A O2A O 0 1 N N N 83.527 64.051 1.540 5.186 -1.905 0.445 O2A TDK 8 TDK O7 O7 O 0 1 N N N 82.507 62.636 -0.313 3.794 0.101 -0.530 O7 TDK 9 TDK C7 C7 C 0 1 N N N 81.181 62.605 0.252 2.486 -0.094 0.012 C7 TDK 10 TDK C6 C6 C 0 1 N N N 80.300 61.963 -0.809 1.440 0.400 -0.989 C6 TDK 11 TDK C5 C5 C 0 1 Y N N 78.784 62.097 -0.682 0.061 0.194 -0.418 C5 TDK 12 TDK S1 S1 S 0 1 Y N N 77.964 61.181 0.542 -0.938 -1.245 -0.611 S1 TDK 13 TDK C4 C4 C 0 1 Y N N 77.837 62.828 -1.403 -0.619 1.069 0.330 C4 TDK 14 TDK CM4 CM4 C 0 1 N N N 78.284 63.740 -2.531 -0.068 2.420 0.707 CM4 TDK 15 TDK N3 N3 N 1 1 Y N N 76.527 62.645 -1.006 -1.810 0.653 0.711 N3 TDK 16 TDK C2 C2 C 0 1 Y N N 76.403 61.765 0.040 -2.172 -0.524 0.327 C2 TDK 17 TDK CMA CMA C 0 1 N N S 75.068 61.293 0.629 -3.491 -1.172 0.661 CMA TDK 18 TDK OM1 OM1 O 0 1 N N N 74.111 62.350 0.744 -4.551 -0.242 0.431 OM1 TDK 19 TDK CMB CMB C 0 1 N N N 75.247 60.637 2.000 -3.494 -1.594 2.132 CMB TDK 20 TDK PC PC P 0 1 N N R 74.323 60.027 -0.514 -3.731 -2.640 -0.393 PC TDK 21 TDK OM3 OM3 O 0 1 N N N 75.119 58.739 -0.487 -2.471 -3.629 -0.231 OM3 TDK 22 TDK OM2 OM2 O 0 1 N N N 72.886 59.581 0.101 -5.075 -3.407 0.053 OM2 TDK 23 TDK CMC CMC C 0 1 N N N 72.180 58.484 -0.492 -5.594 -4.539 -0.648 CMC TDK 24 TDK OM4 OM4 O 0 1 N N N 74.072 60.594 -1.894 -3.849 -2.219 -1.806 OM4 TDK 25 TDK "C7'" C7* C 0 1 N N N 75.420 63.403 -1.621 -2.684 1.491 1.536 "C7'" TDK 26 TDK "C5'" C5* C 0 1 Y N N 75.500 64.874 -1.130 -3.674 2.206 0.653 "C5'" TDK 27 TDK "C6'" C6* C 0 1 Y N N 75.660 65.921 -2.060 -3.248 3.110 -0.300 "C6'" TDK 28 TDK "N1'" N1* N 0 1 Y N N 75.737 67.213 -1.661 -4.147 3.721 -1.059 "N1'" TDK 29 TDK "C2'" C2* C 0 1 Y N N 75.666 67.538 -0.353 -5.434 3.477 -0.917 "C2'" TDK 30 TDK CM2 CM2 C 0 1 N N N 75.758 68.983 0.059 -6.418 4.196 -1.804 CM2 TDK 31 TDK "N3'" N3* N 0 1 Y N N 75.524 66.582 0.589 -5.885 2.622 -0.021 "N3'" TDK 32 TDK "C4'" C4* C 0 1 Y N N 75.435 65.259 0.222 -5.044 1.967 0.774 "C4'" TDK 33 TDK "N4'" N4* N 0 1 N N N 75.284 64.366 1.229 -5.521 1.065 1.712 "N4'" TDK 34 TDK H2B H2B H 0 1 N N N 86.299 59.733 1.965 7.899 2.490 0.210 H2B TDK 35 TDK H3B H3B H 0 1 N N N 84.698 60.300 -0.949 9.773 0.599 -1.487 H3B TDK 36 TDK H2A H2A H 0 1 N N N 83.468 63.724 2.430 5.181 -2.399 -0.386 H2A TDK 37 TDK H71 1H7 H 0 1 N N N 80.829 63.613 0.516 2.329 -1.154 0.209 H71 TDK 38 TDK H72 2H7 H 0 1 N N N 81.166 62.016 1.181 2.391 0.467 0.942 H72 TDK 39 TDK H61 1H6 H 0 1 N N N 80.488 60.884 -0.704 1.597 1.460 -1.187 H61 TDK 40 TDK H62 2H6 H 0 1 N N N 80.576 62.428 -1.767 1.535 -0.161 -1.920 H62 TDK 41 TDK HM41 1HM4 H 0 0 N N N 77.533 63.723 -3.335 -0.347 3.151 -0.052 HM41 TDK 42 TDK HM42 2HM4 H 0 0 N N N 79.250 63.391 -2.924 -0.476 2.723 1.671 HM42 TDK 43 TDK HM43 3HM4 H 0 0 N N N 78.392 64.767 -2.152 1.019 2.363 0.774 HM43 TDK 44 TDK HM1 HM1 H 0 1 N N N 73.899 62.487 1.660 -4.681 -0.017 -0.501 HM1 TDK 45 TDK HMB1 1HMB H 0 0 N N N 74.398 60.902 2.647 -3.271 -0.731 2.758 HMB1 TDK 46 TDK HMB2 2HMB H 0 0 N N N 76.182 60.993 2.457 -4.475 -1.990 2.395 HMB2 TDK 47 TDK HMB3 3HMB H 0 0 N N N 75.290 59.544 1.881 -2.738 -2.363 2.291 HMB3 TDK 48 TDK HM3 HM3 H 0 1 N N N 75.286 58.451 -1.377 -2.333 -3.946 0.672 HM3 TDK 49 TDK HMC1 1HMC H 0 0 N N N 71.218 58.346 0.023 -6.507 -4.881 -0.160 HMC1 TDK 50 TDK HMC2 2HMC H 0 0 N N N 72.781 57.568 -0.398 -5.817 -4.258 -1.678 HMC2 TDK 51 TDK HMC3 3HMC H 0 0 N N N 71.999 58.696 -1.556 -4.856 -5.340 -0.642 HMC3 TDK 52 TDK "H7'1" 1H7* H 0 0 N N N 74.455 62.961 -1.333 -3.220 0.864 2.249 "H7'1" TDK 53 TDK "H7'2" 2H7* H 0 0 N N N 75.509 63.370 -2.717 -2.082 2.223 2.075 "H7'2" TDK 54 TDK "H6'" H6* H 0 1 N N N 75.723 65.688 -3.113 -2.196 3.318 -0.425 "H6'" TDK 55 TDK HM21 1HM2 H 0 0 N N N 74.884 69.530 -0.324 -6.588 3.610 -2.707 HM21 TDK 56 TDK HM22 2HM2 H 0 0 N N N 76.677 69.424 -0.354 -7.361 4.324 -1.271 HM22 TDK 57 TDK HM23 3HM2 H 0 0 N N N 75.780 69.051 1.157 -6.018 5.173 -2.074 HM23 TDK 58 TDK "H4'1" 1H4* H 0 0 N N N 75.233 64.593 2.202 -4.920 0.419 2.112 "H4'1" TDK 59 TDK "H4'2" 2H4* H 0 0 N N N 75.231 63.444 0.846 -6.457 1.081 1.967 "H4'2" TDK 60 # # 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 TDK O2B PB SING N N 1 TDK O2B H2B SING N N 2 TDK PB O3B SING N N 3 TDK PB O1B DOUB N N 4 TDK PB O3A SING N N 5 TDK O3B H3B SING N N 6 TDK O3A PA SING N N 7 TDK PA O1A DOUB N N 8 TDK PA O2A SING N N 9 TDK PA O7 SING N N 10 TDK O2A H2A SING N N 11 TDK O7 C7 SING N N 12 TDK C7 C6 SING N N 13 TDK C7 H71 SING N N 14 TDK C7 H72 SING N N 15 TDK C6 C5 SING N N 16 TDK C6 H61 SING N N 17 TDK C6 H62 SING N N 18 TDK C5 S1 SING Y N 19 TDK C5 C4 DOUB Y N 20 TDK S1 C2 SING Y N 21 TDK C4 CM4 SING N N 22 TDK C4 N3 SING Y N 23 TDK CM4 HM41 SING N N 24 TDK CM4 HM42 SING N N 25 TDK CM4 HM43 SING N N 26 TDK N3 C2 DOUB Y N 27 TDK N3 "C7'" SING N N 28 TDK C2 CMA SING N N 29 TDK CMA OM1 SING N N 30 TDK CMA CMB SING N N 31 TDK CMA PC SING N N 32 TDK OM1 HM1 SING N N 33 TDK CMB HMB1 SING N N 34 TDK CMB HMB2 SING N N 35 TDK CMB HMB3 SING N N 36 TDK PC OM3 SING N N 37 TDK PC OM2 SING N N 38 TDK PC OM4 DOUB N N 39 TDK OM3 HM3 SING N N 40 TDK OM2 CMC SING N N 41 TDK CMC HMC1 SING N N 42 TDK CMC HMC2 SING N N 43 TDK CMC HMC3 SING N N 44 TDK "C7'" "C5'" SING N N 45 TDK "C7'" "H7'1" SING N N 46 TDK "C7'" "H7'2" SING N N 47 TDK "C5'" "C6'" DOUB Y N 48 TDK "C5'" "C4'" SING Y N 49 TDK "C6'" "N1'" SING Y N 50 TDK "C6'" "H6'" SING N N 51 TDK "N1'" "C2'" DOUB Y N 52 TDK "C2'" CM2 SING N N 53 TDK "C2'" "N3'" SING Y N 54 TDK CM2 HM21 SING N N 55 TDK CM2 HM22 SING N N 56 TDK CM2 HM23 SING N N 57 TDK "N3'" "C4'" DOUB Y N 58 TDK "C4'" "N4'" SING N N 59 TDK "N4'" "H4'1" SING N N 60 TDK "N4'" "H4'2" SING N N 61 # # 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 TDK SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCCc1sc([n+](c1C)Cc2cnc(nc2N)C)C(O)(P(=O)(OC)O)C" TDK InChI InChI 1.03 "InChI=1S/C15H25N4O11P3S/c1-9-12(5-6-29-33(26,27)30-32(23,24)25)34-14(15(3,20)31(21,22)28-4)19(9)8-11-7-17-10(2)18-13(11)16/h7,20H,5-6,8H2,1-4H3,(H5-,16,17,18,21,22,23,24,25,26,27)/p+1/t15-/m0/s1" TDK InChIKey InChI 1.03 ILGXNMPRCMTAOK-HNNXBMFYSA-O TDK SMILES_CANONICAL CACTVS 3.385 "CO[P](O)(=O)[C@](C)(O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N" TDK SMILES CACTVS 3.385 "CO[P](O)(=O)[C](C)(O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N" TDK SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](C)(O)[P@@](=O)(O)OC)CCO[P@@](=O)(O)OP(=O)(O)O" TDK SMILES "OpenEye OEToolkits" 1.7.5 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(C)(O)P(=O)(O)OC)CCOP(=O)(O)OP(=O)(O)O" # # 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 TDK "SYSTEMATIC NAME" ACDLabs 10.04 "3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(1S)-1-hydroxy-1-[(R)-hydroxy(methoxy)phosphoryl]ethyl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium" TDK "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(1S)-1-[3-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-5-[2-(hydroxy-phosphonooxy-phosphoryl)oxyethyl]-4-methyl-1,3-thiazol-3-ium-2-yl]-1-hydroxy-ethyl]-methoxy-phosphinic 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 TDK "Create component" 2005-12-01 PDBJ TDK "Modify descriptor" 2011-06-04 RCSB TDK "Modify descriptor" 2012-01-05 RCSB TDK "Modify coordinates" 2012-01-05 RCSB TDK "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id TDK _pdbx_chem_comp_synonyms.name "2-PHOSPHONOLACTYLTHIAMIN DIPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##