data_TD5 # _chem_comp.id TD5 _chem_comp.name "(4~{R})-4-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-4-oxidanyl-butanoic acid" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H25 N4 O10 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2015-11-20 _chem_comp.pdbx_modified_date 2016-10-28 _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 527.403 _chem_comp.one_letter_code ? _chem_comp.three_letter_code TD5 _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 5EJM _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 TD5 S1 S1 S 0 1 Y N N -13.962 -8.702 -27.928 -1.406 1.942 -0.438 S1 TD5 1 TD5 C2 C1 C 0 1 Y N N -14.514 -8.330 -26.317 -2.689 0.874 -0.068 C2 TD5 2 TD5 N3 N1 N 1 1 Y N N -15.237 -9.389 -25.859 -2.313 0.020 0.823 N3 TD5 3 TD5 C4 C2 C 0 1 Y N N -15.324 -10.439 -26.707 -1.076 0.119 1.266 C4 TD5 4 TD5 C5 C3 C 0 1 Y N N -14.666 -10.291 -27.938 -0.368 1.110 0.717 C5 TD5 5 TD5 C6 C4 C 0 1 N N N -14.577 -11.316 -29.109 1.065 1.456 1.030 C6 TD5 6 TD5 C7 C5 C 0 1 N N N -15.297 -10.914 -30.441 1.993 0.680 0.093 C7 TD5 7 TD5 O7 O1 O 0 1 N N N -14.965 -11.994 -31.257 3.352 1.008 0.391 O7 TD5 8 TD5 PA P1 P 0 1 N N N -15.111 -11.794 -32.817 4.601 0.373 -0.403 PA TD5 9 TD5 PB P2 P 0 1 N N N -12.464 -10.750 -33.168 7.507 0.377 0.182 PB TD5 10 TD5 "N1'" N2 N 0 1 Y N N -19.600 -10.064 -24.310 -2.079 -3.422 -1.273 "N1'" TD5 11 TD5 C11 C6 C 0 1 N N R -14.212 -7.071 -25.528 -4.059 0.923 -0.693 C11 TD5 12 TD5 C13 C7 C 0 1 N N N -12.433 -6.548 -23.648 -6.278 2.070 -0.645 C13 TD5 13 TD5 O1A O2 O 0 1 N N N -14.840 -13.122 -33.535 4.522 -1.104 -0.348 O1A TD5 14 TD5 O1B O3 O 0 1 N N N -11.917 -10.638 -31.750 8.320 0.906 1.466 O1B TD5 15 TD5 "C2'" C8 C 0 1 Y N N -20.168 -8.998 -24.915 -2.720 -4.516 -0.915 "C2'" TD5 16 TD5 O2A O4 O 0 1 N N N -16.479 -11.274 -33.100 4.562 0.856 -1.939 O2A TD5 17 TD5 O2B O5 O 0 1 N N N -12.031 -9.577 -34.022 7.554 -1.102 0.143 O2B TD5 18 TD5 "N3'" N3 N 0 1 Y N N -19.400 -8.043 -25.422 -3.520 -4.541 0.132 "N3'" TD5 19 TD5 O3A O6 O 0 1 N N N -14.065 -10.680 -33.244 5.975 0.863 0.278 O3A TD5 20 TD5 O3B O7 O 0 1 N N N -11.986 -12.029 -33.840 8.174 0.971 -1.158 O3B TD5 21 TD5 "C4'" C9 C 0 1 Y N N -18.041 -8.101 -25.317 -3.707 -3.451 0.869 "C4'" TD5 22 TD5 "N4'" N4 N 0 1 N N N -17.374 -7.086 -25.834 -4.549 -3.481 1.970 "N4'" TD5 23 TD5 "C5'" C10 C 0 1 Y N N -17.427 -9.201 -24.692 -3.042 -2.274 0.517 "C5'" TD5 24 TD5 "C6'" C11 C 0 1 Y N N -18.254 -10.187 -24.188 -2.215 -2.295 -0.588 "C6'" TD5 25 TD5 "C7'" C12 C 0 1 N N N -15.893 -9.383 -24.527 -3.223 -1.013 1.323 "C7'" TD5 26 TD5 OL1 O8 O 0 1 N N N -13.692 -6.106 -26.448 -3.933 1.095 -2.106 OL1 TD5 27 TD5 OL2 O9 O 0 1 N N N -12.391 -6.045 -21.333 -8.341 3.405 -0.400 OL2 TD5 28 TD5 OL3 O10 O 0 1 N N N -13.480 -7.831 -21.895 -6.517 3.990 0.701 OL3 TD5 29 TD5 CLB C13 C 0 1 N N N -13.019 -7.572 -24.654 -4.847 2.095 -0.104 CLB TD5 30 TD5 CLC C14 C 0 1 N N N -12.791 -6.831 -22.218 -7.054 3.225 -0.065 CLC TD5 31 TD5 CM2 C15 C 0 1 N N N -21.734 -8.892 -25.046 -2.534 -5.773 -1.725 CM2 TD5 32 TD5 CM4 C16 C 0 1 N N N -16.116 -11.728 -26.337 -0.506 -0.811 2.306 CM4 TD5 33 TD5 H6 H1 H 0 1 N N N -15.019 -12.261 -28.761 1.219 2.526 0.890 H6 TD5 34 TD5 H6A H2 H 0 1 N N N -13.512 -11.472 -29.338 1.286 1.189 2.063 H6A TD5 35 TD5 H7A H3 H 0 1 N N N -14.905 -9.968 -30.843 1.839 -0.390 0.233 H7A TD5 36 TD5 H7 H4 H 0 1 N N N -16.385 -10.831 -30.303 1.773 0.947 -0.940 H7 TD5 37 TD5 H1 H5 H 0 1 N N N -15.062 -6.721 -24.923 -4.586 -0.009 -0.486 H1 TD5 38 TD5 H13 H6 H 0 1 N N N -11.337 -6.560 -23.740 -6.258 2.155 -1.731 H13 TD5 39 TD5 H13A H7 H 0 0 N N N -12.812 -5.549 -23.909 -6.757 1.133 -0.362 H13A TD5 40 TD5 H2 H8 H 0 1 N N N -11.402 -9.844 -31.671 9.252 0.650 1.475 H2 TD5 41 TD5 H3 H9 H 0 1 N N N -16.932 -11.873 -33.681 4.610 1.815 -2.051 H3 TD5 42 TD5 H4 H10 H 0 1 N N N -11.524 -11.813 -34.642 8.178 1.937 -1.201 H4 TD5 43 TD5 "HN4'" H11 H 0 0 N N N -18.018 -6.429 -26.227 -4.939 -4.320 2.258 "HN4'" TD5 44 TD5 HN4A H12 H 0 0 N N N -16.838 -6.640 -25.117 -4.747 -2.663 2.451 HN4A TD5 45 TD5 "H6'" H13 H 0 1 N N N -17.831 -11.052 -23.699 -1.684 -1.404 -0.890 "H6'" TD5 46 TD5 "H7'A" H14 H 0 0 N N N -15.692 -10.337 -24.017 -3.002 -1.217 2.370 "H7'A" TD5 47 TD5 "H7'" H15 H 0 1 N N N -15.490 -8.554 -23.926 -4.253 -0.667 1.229 "H7'" TD5 48 TD5 HOL1 H16 H 0 0 N N N -13.491 -5.302 -25.984 -3.473 1.905 -2.364 HOL1 TD5 49 TD5 H5 H17 H 0 1 N N N -12.691 -6.345 -20.483 -8.797 4.159 -0.003 H5 TD5 50 TD5 HLB H18 H 0 1 N N N -13.365 -8.445 -24.081 -4.867 2.010 0.982 HLB TD5 51 TD5 HLBA H19 H 0 0 N N N -12.209 -7.877 -25.333 -4.368 3.033 -0.387 HLBA TD5 52 TD5 HM2B H20 H 0 0 N N N -21.996 -7.968 -25.582 -1.697 -6.344 -1.323 HM2B TD5 53 TD5 HM2 H21 H 0 1 N N N -22.115 -9.760 -25.604 -3.441 -6.374 -1.676 HM2 TD5 54 TD5 HM2A H22 H 0 0 N N N -22.185 -8.874 -24.043 -2.328 -5.509 -2.763 HM2A TD5 55 TD5 HM4A H23 H 0 0 N N N -15.444 -12.441 -25.836 -0.106 -1.701 1.818 HM4A TD5 56 TD5 HM4B H24 H 0 0 N N N -16.944 -11.468 -25.661 0.293 -0.305 2.847 HM4B TD5 57 TD5 HM4 H25 H 0 1 N N N -16.520 -12.186 -27.252 -1.291 -1.101 3.004 HM4 TD5 58 # 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 TD5 O2B PB DOUB N N 1 TD5 O3B PB SING N N 2 TD5 O1A PA DOUB N N 3 TD5 O3A PB SING N N 4 TD5 O3A PA SING N N 5 TD5 PB O1B SING N N 6 TD5 O2A PA SING N N 7 TD5 PA O7 SING N N 8 TD5 O7 C7 SING N N 9 TD5 C7 C6 SING N N 10 TD5 C6 C5 SING N N 11 TD5 C5 S1 SING Y N 12 TD5 C5 C4 DOUB Y N 13 TD5 S1 C2 SING Y N 14 TD5 C4 CM4 SING N N 15 TD5 C4 N3 SING Y N 16 TD5 OL1 C11 SING N N 17 TD5 C2 N3 DOUB Y N 18 TD5 C2 C11 SING N N 19 TD5 N3 "C7'" SING N N 20 TD5 "N4'" "C4'" SING N N 21 TD5 C11 CLB SING N N 22 TD5 "N3'" "C4'" DOUB Y N 23 TD5 "N3'" "C2'" SING Y N 24 TD5 "C4'" "C5'" SING Y N 25 TD5 CM2 "C2'" SING N N 26 TD5 "C2'" "N1'" DOUB Y N 27 TD5 "C5'" "C7'" SING N N 28 TD5 "C5'" "C6'" DOUB Y N 29 TD5 CLB C13 SING N N 30 TD5 "N1'" "C6'" SING Y N 31 TD5 C13 CLC SING N N 32 TD5 CLC OL3 DOUB N N 33 TD5 CLC OL2 SING N N 34 TD5 C6 H6 SING N N 35 TD5 C6 H6A SING N N 36 TD5 C7 H7A SING N N 37 TD5 C7 H7 SING N N 38 TD5 C11 H1 SING N N 39 TD5 C13 H13 SING N N 40 TD5 C13 H13A SING N N 41 TD5 O1B H2 SING N N 42 TD5 O2A H3 SING N N 43 TD5 O3B H4 SING N N 44 TD5 "N4'" "HN4'" SING N N 45 TD5 "N4'" HN4A SING N N 46 TD5 "C6'" "H6'" SING N N 47 TD5 "C7'" "H7'A" SING N N 48 TD5 "C7'" "H7'" SING N N 49 TD5 OL1 HOL1 SING N N 50 TD5 OL2 H5 SING N N 51 TD5 CLB HLB SING N N 52 TD5 CLB HLBA SING N N 53 TD5 CM2 HM2B SING N N 54 TD5 CM2 HM2 SING N N 55 TD5 CM2 HM2A SING N N 56 TD5 CM4 HM4A SING N N 57 TD5 CM4 HM4B SING N N 58 TD5 CM4 HM4 SING N N 59 # 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 TD5 InChI InChI 1.03 "InChI=1S/C16H24N4O10P2S/c1-9-13(5-6-29-32(27,28)30-31(24,25)26)33-16(12(21)3-4-14(22)23)20(9)8-11-7-18-10(2)19-15(11)17/h7,12,21H,3-6,8H2,1-2H3,(H5-,17,18,19,22,23,24,25,26,27,28)/p+1/t12-/m1/s1" TD5 InChIKey InChI 1.03 ZWUKRGPVMMTMAF-GFCCVEGCSA-O TD5 SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C@H](O)CCC(O)=O)c(N)n1" TD5 SMILES CACTVS 3.385 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[CH](O)CCC(O)=O)c(N)n1" TD5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@H](CCC(=O)O)O)CCOP(=O)(O)OP(=O)(O)O" TD5 SMILES "OpenEye OEToolkits" 2.0.4 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(CCC(=O)O)O)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 TD5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "(4~{R})-4-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-4-oxidanyl-butanoic 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 TD5 "Create component" 2015-11-20 PDBJ TD5 "Initial release" 2016-11-02 RCSB #