data_T5X # _chem_comp.id T5X _chem_comp.name ;2-C-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thia zol-3-ium-2-yl}-5-O-phosphono-D-xylitol ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H30 N4 O15 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "D-XYLULOSE-5-PHOSPHATE THIAMIN DIPHOSPHATE ADDUCT" _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2007-10-25 _chem_comp.pdbx_modified_date 2020-06-17 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 655.424 _chem_comp.one_letter_code ? _chem_comp.three_letter_code T5X _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 2R8O _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 T5X O2A O2A O 0 1 N N N 16.925 -16.658 4.867 -4.744 -2.721 -1.455 O2A T5X 1 T5X PA PA P 0 1 N N R 15.869 -17.597 4.337 -5.304 -1.671 -0.370 PA T5X 2 T5X O1A O1A O 0 1 N N N 15.887 -17.939 2.882 -5.644 -0.399 -1.044 O1A T5X 3 T5X O3A O3A O 0 1 N N N 15.898 -18.912 5.264 -6.622 -2.276 0.331 O3A T5X 4 T5X PB PB P 0 1 N N N 15.473 -20.449 4.988 -8.150 -2.468 -0.138 PB T5X 5 T5X O3B O3B O 0 1 N N N 16.262 -21.143 6.053 -8.901 -1.045 -0.116 O3B T5X 6 T5X O2B O2B O 0 1 N N N 15.845 -20.882 3.600 -8.179 -3.020 -1.511 O2B T5X 7 T5X O1B O1B O 0 1 N N N 13.962 -20.427 5.132 -8.895 -3.484 0.864 O1B T5X 8 T5X O7 O7 O 0 1 N N N 14.435 -16.973 4.634 -4.177 -1.402 0.748 O7 T5X 9 T5X C7 C7 C 0 1 N N N 14.337 -16.341 5.904 -2.929 -0.770 0.458 C7 T5X 10 T5X C6 C6 C 0 1 N N N 12.918 -15.869 6.082 -2.098 -0.671 1.739 C6 T5X 11 T5X C5 C5 C 0 1 Y N N 12.830 -15.272 7.458 -0.781 -0.005 1.433 C5 T5X 12 T5X S1 S1 S 0 1 Y N N 13.236 -16.227 8.922 0.702 -0.818 0.938 S1 T5X 13 T5X C2 C2 C 0 1 Y N N 12.430 -15.025 9.987 1.509 0.687 0.856 C2 T5X 14 T5X CX2 CX2 C 0 1 N N S 11.983 -15.466 11.364 2.954 0.870 0.467 CX2 T5X 15 T5X CX3 CX3 C 0 1 N N S 10.610 -16.163 11.229 3.618 -0.499 0.312 CX3 T5X 16 T5X CX4 CX4 C 0 1 N N R 9.774 -16.228 12.516 5.113 -0.313 0.045 CX4 T5X 17 T5X CX5 CX5 C 0 1 N N N 8.334 -16.628 12.217 5.800 -1.680 0.021 CX5 T5X 18 T5X OX5 OX5 O 0 1 N N N 7.519 -16.371 13.367 7.212 -1.501 -0.113 OX5 T5X 19 T5X PX PX P 0 1 N N N 6.080 -17.072 13.543 8.250 -2.730 -0.173 PX T5X 20 T5X OX7 OX7 O 0 1 N N N 5.330 -16.827 12.257 8.064 -3.591 1.016 OX7 T5X 21 T5X OX6 OX6 O 0 1 N N N 5.493 -16.375 14.747 7.985 -3.592 -1.507 OX6 T5X 22 T5X OX8 OX8 O 0 1 N N N 6.383 -18.543 13.768 9.756 -2.160 -0.192 OX8 T5X 23 T5X OX4 OX4 O 0 1 N N N 10.305 -17.186 13.438 5.295 0.334 -1.216 OX4 T5X 24 T5X OX3 OX3 O 0 1 N N N 10.747 -17.489 10.684 3.022 -1.197 -0.783 OX3 T5X 25 T5X CX1 CX1 C 0 1 N N N 13.048 -16.351 12.022 3.032 1.628 -0.859 CX1 T5X 26 T5X OX1 OX1 O 0 1 N N N 14.227 -15.606 12.385 2.308 0.912 -1.861 OX1 T5X 27 T5X OX2 OX2 O 0 1 N N N 11.838 -14.296 12.174 3.629 1.615 1.482 OX2 T5X 28 T5X N3 N3 N 1 1 Y N N 12.088 -14.016 9.152 0.703 1.642 1.175 N3 T5X 29 T5X C4 C4 C 0 1 Y N N 12.171 -14.113 7.814 -0.534 1.307 1.484 C4 T5X 30 T5X CM4 CM4 C 0 1 N N N 11.528 -13.250 6.755 -1.581 2.320 1.867 CM4 T5X 31 T5X "C7," "C7," C 0 1 N N N 11.704 -12.713 9.690 1.142 3.040 1.187 "C7," T5X 32 T5X "C5," "C5," C 0 1 Y N N 12.785 -11.645 9.645 0.298 3.839 0.227 "C5," T5X 33 T5X "C4," "C4," C 0 1 Y N N 13.990 -11.700 10.368 -0.632 4.769 0.695 "C4," T5X 34 T5X "N4," "N4," N 0 1 N N N 14.319 -12.734 11.179 -0.798 4.976 2.055 "N4," T5X 35 T5X "N3," "N3," N 0 1 Y N N 14.891 -10.689 10.275 -1.356 5.455 -0.185 "N3," T5X 36 T5X "C2," "C2," C 0 1 Y N N 14.621 -9.624 9.503 -1.201 5.261 -1.479 "C2," T5X 37 T5X CM2 CM2 C 0 1 N N N 15.608 -8.496 9.424 -2.040 6.057 -2.445 CM2 T5X 38 T5X "N1," "N1," N 0 1 Y N N 13.466 -9.548 8.807 -0.331 4.391 -1.952 "N1," T5X 39 T5X "C6," "C6," C 0 1 Y N N 12.547 -10.526 8.854 0.430 3.674 -1.138 "C6," T5X 40 T5X HO2A HO2A H 0 0 N N N 17.549 -16.461 4.178 -4.501 -3.579 -1.082 HO2A T5X 41 T5X HO3B HO3B H 0 0 N N N 17.149 -21.290 5.746 -8.921 -0.624 0.754 HO3B T5X 42 T5X HO1B HO1B H 0 0 N N N 13.731 -20.422 6.054 -9.822 -3.647 0.641 HO1B T5X 43 T5X H71 1H7 H 0 1 N N N 14.598 -17.055 6.699 -2.387 -1.359 -0.282 H71 T5X 44 T5X H72 2H7 H 0 1 N N N 15.032 -15.490 5.961 -3.111 0.230 0.064 H72 T5X 45 T5X H61 1H6 H 0 1 N N N 12.666 -15.116 5.321 -2.640 -0.082 2.479 H61 T5X 46 T5X H62 2H6 H 0 1 N N N 12.208 -16.702 5.968 -1.916 -1.671 2.133 H62 T5X 47 T5X HX3 HX3 H 0 1 N N N 10.054 -15.514 10.536 3.481 -1.075 1.227 HX3 T5X 48 T5X HX4 HX4 H 0 1 N N N 9.808 -15.221 12.958 5.550 0.299 0.834 HX4 T5X 49 T5X HX51 1HX5 H 0 0 N N N 7.960 -16.042 11.364 5.588 -2.210 0.949 HX51 T5X 50 T5X HX52 2HX5 H 0 0 N N N 8.294 -17.699 11.971 5.427 -2.260 -0.823 HX52 T5X 51 T5X HOX6 HOX6 H 0 0 N N N 5.370 -17.004 15.449 8.089 -3.090 -2.326 HOX6 T5X 52 T5X HOX8 HOX8 H 0 0 N N N 6.446 -18.986 12.930 10.436 -2.847 -0.228 HOX8 T5X 53 T5X HOX4 HOX4 H 0 0 N N N 10.423 -18.019 12.997 4.930 -0.156 -1.966 HOX4 T5X 54 T5X HOX3 HOX3 H 0 0 N N N 10.777 -17.441 9.736 3.220 -0.813 -1.648 HOX3 T5X 55 T5X HX11 1HX1 H 0 0 N N N 12.620 -16.795 12.933 2.598 2.621 -0.737 HX11 T5X 56 T5X HX12 2HX1 H 0 0 N N N 13.344 -17.122 11.295 4.075 1.723 -1.163 HX12 T5X 57 T5X HOX1 HOX1 H 0 0 N N N 14.750 -15.442 11.609 2.315 1.335 -2.730 HOX1 T5X 58 T5X HOX2 HOX2 H 0 0 N N N 11.806 -14.546 13.090 3.619 1.193 2.352 HOX2 T5X 59 T5X HM41 1HM4 H 0 0 N N N 11.372 -12.236 7.152 -1.464 2.584 2.918 HM41 T5X 60 T5X HM42 2HM4 H 0 0 N N N 12.185 -13.201 5.874 -1.464 3.214 1.254 HM42 T5X 61 T5X HM43 3HM4 H 0 0 N N N 10.559 -13.684 6.467 -2.572 1.896 1.707 HM43 T5X 62 T5X "H7,1" "1H7," H 0 0 N N N 10.852 -12.348 9.098 1.032 3.447 2.192 "H7,1" T5X 63 T5X "H7,2" "2H7," H 0 0 N N N 11.477 -12.875 10.754 2.187 3.095 0.884 "H7,2" T5X 64 T5X "H4,1" "1H4," H 0 0 N N N 14.400 -13.571 10.637 -0.175 4.581 2.685 "H4,1" T5X 65 T5X "H4,2" "2H4," H 0 0 N N N 15.192 -12.541 11.627 -1.536 5.515 2.377 "H4,2" T5X 66 T5X HM21 1HM2 H 0 0 N N N 15.849 -8.148 10.439 -1.522 6.981 -2.701 HM21 T5X 67 T5X HM22 2HM2 H 0 0 N N N 16.526 -8.846 8.929 -2.207 5.472 -3.349 HM22 T5X 68 T5X HM23 3HM2 H 0 0 N N N 15.172 -7.668 8.846 -2.999 6.294 -1.983 HM23 T5X 69 T5X "H6," "H6," H 0 1 N N N 11.633 -10.445 8.284 1.140 2.964 -1.537 "H6," T5X 70 # # 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 T5X O1A PA DOUB N N 1 T5X O2B PB DOUB N N 2 T5X PA O7 SING N N 3 T5X PA O2A SING N N 4 T5X PA O3A SING N N 5 T5X O7 C7 SING N N 6 T5X PB O1B SING N N 7 T5X PB O3A SING N N 8 T5X PB O3B SING N N 9 T5X C7 C6 SING N N 10 T5X C6 C5 SING N N 11 T5X CM4 C4 SING N N 12 T5X C5 C4 DOUB Y N 13 T5X C5 S1 SING Y N 14 T5X C4 N3 SING Y N 15 T5X "N1," "C6," DOUB Y N 16 T5X "N1," "C2," SING Y N 17 T5X "C6," "C5," SING Y N 18 T5X S1 C2 SING Y N 19 T5X N3 "C7," SING N N 20 T5X N3 C2 DOUB Y N 21 T5X CM2 "C2," SING N N 22 T5X "C2," "N3," DOUB Y N 23 T5X "C5," "C7," SING N N 24 T5X "C5," "C4," DOUB Y N 25 T5X C2 CX2 SING N N 26 T5X "N3," "C4," SING Y N 27 T5X "C4," "N4," SING N N 28 T5X OX3 CX3 SING N N 29 T5X CX3 CX2 SING N N 30 T5X CX3 CX4 SING N N 31 T5X CX2 CX1 SING N N 32 T5X CX2 OX2 SING N N 33 T5X CX1 OX1 SING N N 34 T5X CX5 CX4 SING N N 35 T5X CX5 OX5 SING N N 36 T5X OX7 PX DOUB N N 37 T5X CX4 OX4 SING N N 38 T5X OX5 PX SING N N 39 T5X PX OX8 SING N N 40 T5X PX OX6 SING N N 41 T5X O2A HO2A SING N N 42 T5X O3B HO3B SING N N 43 T5X O1B HO1B SING N N 44 T5X C7 H71 SING N N 45 T5X C7 H72 SING N N 46 T5X C6 H61 SING N N 47 T5X C6 H62 SING N N 48 T5X CX3 HX3 SING N N 49 T5X CX4 HX4 SING N N 50 T5X CX5 HX51 SING N N 51 T5X CX5 HX52 SING N N 52 T5X OX6 HOX6 SING N N 53 T5X OX8 HOX8 SING N N 54 T5X OX4 HOX4 SING N N 55 T5X OX3 HOX3 SING N N 56 T5X CX1 HX11 SING N N 57 T5X CX1 HX12 SING N N 58 T5X OX1 HOX1 SING N N 59 T5X OX2 HOX2 SING N N 60 T5X CM4 HM41 SING N N 61 T5X CM4 HM42 SING N N 62 T5X CM4 HM43 SING N N 63 T5X "C7," "H7,1" SING N N 64 T5X "C7," "H7,2" SING N N 65 T5X "N4," "H4,1" SING N N 66 T5X "N4," "H4,2" SING N N 67 T5X CM2 HM21 SING N N 68 T5X CM2 HM22 SING N N 69 T5X CM2 HM23 SING N N 70 T5X "C6," "H6," SING N N 71 # # 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 T5X SMILES ACDLabs 10.04 "O=P(O)(O)OCC(O)C(O)C(O)(c1sc(c([n+]1Cc2cnc(nc2N)C)C)CCOP(=O)(O)OP(=O)(O)O)CO" T5X SMILES_CANONICAL CACTVS 3.341 "Cc1ncc(C[n+]2c(C)c(CCO[P@](O)(=O)O[P](O)(O)=O)sc2[C@](O)(CO)[C@@H](O)[C@H](O)CO[P](O)(O)=O)c(N)n1" T5X SMILES CACTVS 3.341 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C](O)(CO)[CH](O)[CH](O)CO[P](O)(O)=O)c(N)n1" T5X SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@](CO)([C@H]([C@@H](COP(=O)(O)O)O)O)O)CCO[P@@](=O)(O)OP(=O)(O)O" T5X SMILES "OpenEye OEToolkits" 1.5.0 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(CO)(C(C(COP(=O)(O)O)O)O)O)CCOP(=O)(O)OP(=O)(O)O" T5X InChI InChI 1.03 "InChI=1S/C17H29N4O15P3S/c1-9-13(3-4-34-39(32,33)36-38(29,30)31)40-16(21(9)6-11-5-19-10(2)20-15(11)18)17(25,8-22)14(24)12(23)7-35-37(26,27)28/h5,12,14,22-25H,3-4,6-8H2,1-2H3,(H6-,18,19,20,26,27,28,29,30,31,32,33)/p+1/t12-,14+,17+/m1/s1" T5X InChIKey InChI 1.03 CRLXIEJPMQNLRP-IFIJOSMWSA-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 T5X "SYSTEMATIC NAME" ACDLabs 10.04 "2-C-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium-2-yl}-5-O-phosphono-D-xylitol" T5X "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "2-[3-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-[(2S,3S,4R)-1,2,3,4-tetrahydroxy-5-phosphonooxy-pentan-2-yl]-1,3-thiazol-3-ium-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 T5X "Create component" 2007-10-25 RCSB T5X "Modify aromatic_flag" 2011-06-04 RCSB T5X "Modify descriptor" 2011-06-04 RCSB T5X "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id T5X _pdbx_chem_comp_synonyms.name "D-XYLULOSE-5-PHOSPHATE THIAMIN DIPHOSPHATE ADDUCT" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##