data_A5X # _chem_comp.id A5X _chem_comp.name "3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(1S)-1-hydroxy-1-[(R)-hydroxy(oxo)-lambda~5~-phosphanyl]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 "C14 H24 N4 O10 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2018-02-19 _chem_comp.pdbx_modified_date 2018-07-06 _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 533.347 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A5X _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 6CFO _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 A5X O22 O1 O 0 1 N N N 21.126 10.984 -39.023 -8.396 0.608 1.815 O22 A5X 1 A5X P2 P1 P 0 1 N N N 21.722 11.255 -40.404 -7.721 0.177 0.418 P2 A5X 2 A5X O23 O2 O 0 1 N N N 22.967 10.421 -40.578 -7.879 -1.282 0.224 O23 A5X 3 A5X O21 O3 O 0 1 N N N 22.093 12.728 -40.497 -8.441 0.960 -0.790 O21 A5X 4 A5X O11 O4 O 0 1 N N N 20.631 10.944 -41.500 -6.155 0.550 0.442 O11 A5X 5 A5X P1 P2 P 0 1 N N N 20.497 9.640 -42.325 -4.892 0.129 -0.463 P1 A5X 6 A5X O12 O5 O 0 1 N N N 21.818 9.227 -43.015 -4.890 0.997 -1.819 O12 A5X 7 A5X O13 O6 O 0 1 N N N 19.456 9.872 -43.396 -4.983 -1.310 -0.799 O13 A5X 8 A5X O5G O7 O 0 1 N N N 19.980 8.492 -41.417 -3.532 0.404 0.353 O5G A5X 9 A5X C5B C1 C 0 1 N N N 18.660 8.389 -41.036 -2.241 0.038 -0.139 C5B A5X 10 A5X C5A C2 C 0 1 N N N 18.298 7.283 -39.978 -1.173 0.442 0.880 C5A A5X 11 A5X C5 C3 C 0 1 Y N N 17.055 7.396 -39.122 0.188 0.055 0.361 C5 A5X 12 A5X C4 C4 C 0 1 Y N N 15.955 6.477 -39.044 0.990 0.818 -0.388 C4 A5X 13 A5X C4A C5 C 0 1 N N N 15.973 5.224 -39.909 0.617 2.212 -0.822 C4A A5X 14 A5X S1 S1 S 0 1 Y N N 16.670 8.642 -38.030 1.006 -1.480 0.642 S1 A5X 15 A5X C2 C6 C 0 1 Y N N 15.160 8.058 -37.470 2.342 -0.946 -0.282 C2 A5X 16 A5X C2B C7 C 0 1 N N S 14.460 8.813 -36.481 3.585 -1.756 -0.549 C2B A5X 17 A5X P3 P3 P 0 1 N N N 14.799 8.190 -34.770 3.614 -3.207 0.554 P3 A5X 18 A5X O32 O8 O 0 1 N N N 16.357 8.194 -34.446 3.613 -2.755 1.963 O32 A5X 19 A5X O31 O9 O 0 1 N N N 14.238 6.724 -34.549 4.942 -4.071 0.269 O31 A5X 20 A5X C22 C8 C 0 1 N N N 14.312 10.302 -36.684 3.586 -2.223 -2.006 C22 A5X 21 A5X O24 O10 O 0 1 N N N 13.102 8.478 -36.500 4.740 -0.950 -0.307 O24 A5X 22 A5X N3 N1 N 1 1 Y N N 14.922 6.841 -38.145 2.133 0.251 -0.715 N3 A5X 23 A5X C35 C9 C 0 1 N N N 13.727 5.982 -37.995 3.126 0.952 -1.534 C35 A5X 24 A5X "C5'" C10 C 0 1 Y N N 12.799 6.171 -39.197 4.080 1.698 -0.637 "C5'" A5X 25 A5X "C6'" C11 C 0 1 Y N N 12.612 5.137 -40.108 3.615 2.621 0.279 "C6'" A5X 26 A5X "N1'" N2 N 0 1 Y N N 11.798 5.326 -41.180 4.483 3.259 1.052 "N1'" A5X 27 A5X "C2'" C12 C 0 1 Y N N 11.155 6.500 -41.380 5.776 3.025 0.958 "C2'" A5X 28 A5X C2A C13 C 0 1 N N N 10.238 6.673 -42.598 6.724 3.774 1.858 C2A A5X 29 A5X "N3'" N3 N 0 1 Y N N 11.310 7.520 -40.524 6.264 2.152 0.099 "N3'" A5X 30 A5X "C4'" C14 C 0 1 Y N N 12.103 7.406 -39.446 5.456 1.470 -0.707 "C4'" A5X 31 A5X "N4'" N4 N 0 1 N N N 12.218 8.539 -38.567 5.972 0.554 -1.609 "N4'" A5X 32 A5X H1 H1 H 0 1 N N N 21.663 10.349 -38.565 -9.342 0.413 1.871 H1 A5X 33 A5X H2 H2 H 0 1 N N N 23.028 12.811 -40.645 -8.378 1.923 -0.728 H2 A5X 34 A5X H3 H3 H 0 1 N N N 21.692 9.208 -43.956 -4.832 1.952 -1.674 H3 A5X 35 A5X H4 H4 H 0 1 N N N 18.361 9.360 -40.614 -2.204 -1.040 -0.295 H4 A5X 36 A5X H5 H5 H 0 1 N N N 18.070 8.186 -41.942 -2.053 0.548 -1.083 H5 A5X 37 A5X H6 H6 H 0 1 N N N 18.210 6.337 -40.533 -1.210 1.520 1.036 H6 A5X 38 A5X H7 H7 H 0 1 N N N 19.150 7.223 -39.285 -1.361 -0.069 1.825 H7 A5X 39 A5X H8 H8 H 0 1 N N N 16.460 4.405 -39.359 0.959 2.929 -0.075 H8 A5X 40 A5X H9 H9 H 0 1 N N N 14.941 4.936 -40.158 1.087 2.432 -1.780 H9 A5X 41 A5X H10 H10 H 0 1 N N N 16.531 5.426 -40.835 -0.466 2.283 -0.924 H10 A5X 42 A5X H12 H12 H 0 1 N N N 14.944 6.153 -34.270 5.023 -4.860 0.822 H12 A5X 43 A5X H13 H13 H 0 1 N N N 13.753 10.734 -35.841 3.465 -1.362 -2.664 H13 A5X 44 A5X H14 H14 H 0 1 N N N 15.308 10.765 -36.739 4.531 -2.719 -2.228 H14 A5X 45 A5X H15 H15 H 0 1 N N N 13.767 10.492 -37.621 2.764 -2.920 -2.165 H15 A5X 46 A5X H16 H16 H 0 1 N N N 12.642 8.983 -35.840 4.850 -0.689 0.618 H16 A5X 47 A5X H17 H17 H 0 1 N N N 13.192 6.258 -37.074 3.681 0.228 -2.131 H17 A5X 48 A5X H18 H18 H 0 1 N N N 14.039 4.929 -37.937 2.621 1.657 -2.194 H18 A5X 49 A5X H19 H19 H 0 1 N N N 13.110 4.190 -39.965 2.557 2.821 0.364 H19 A5X 50 A5X H20 H20 H 0 1 N N N 10.230 5.744 -43.187 6.869 3.213 2.781 H20 A5X 51 A5X H21 H21 H 0 1 N N N 9.217 6.900 -42.259 7.682 3.899 1.354 H21 A5X 52 A5X H22 H22 H 0 1 N N N 10.609 7.499 -43.222 6.305 4.754 2.091 H22 A5X 53 A5X H23 H23 H 0 1 N N N 11.654 9.289 -38.913 6.893 0.630 -1.905 H23 A5X 54 A5X H24 H24 H 0 1 N N N 11.907 8.283 -37.652 5.413 -0.164 -1.946 H24 A5X 55 A5X H25 H25 H 0 1 N N N 14.138 9.081 -33.883 2.466 -4.008 0.313 H25 A5X 56 # 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 A5X O13 P1 DOUB N N 1 A5X O12 P1 SING N N 2 A5X C2A "C2'" SING N N 3 A5X P1 O11 SING N N 4 A5X P1 O5G SING N N 5 A5X O11 P2 SING N N 6 A5X O5G C5B SING N N 7 A5X "C2'" "N1'" DOUB Y N 8 A5X "C2'" "N3'" SING Y N 9 A5X "N1'" "C6'" SING Y N 10 A5X C5B C5A SING N N 11 A5X O23 P2 DOUB N N 12 A5X "N3'" "C4'" DOUB Y N 13 A5X O21 P2 SING N N 14 A5X P2 O22 SING N N 15 A5X "C6'" "C5'" DOUB Y N 16 A5X C5A C5 SING N N 17 A5X C4A C4 SING N N 18 A5X "C4'" "C5'" SING Y N 19 A5X "C4'" "N4'" SING N N 20 A5X "C5'" C35 SING N N 21 A5X C5 C4 DOUB Y N 22 A5X C5 S1 SING Y N 23 A5X C4 N3 SING Y N 24 A5X N3 C35 SING N N 25 A5X N3 C2 DOUB Y N 26 A5X S1 C2 SING Y N 27 A5X C2 C2B SING N N 28 A5X C22 C2B SING N N 29 A5X O24 C2B SING N N 30 A5X C2B P3 SING N N 31 A5X P3 O31 SING N N 32 A5X P3 O32 DOUB N N 33 A5X O22 H1 SING N N 34 A5X O21 H2 SING N N 35 A5X O12 H3 SING N N 36 A5X C5B H4 SING N N 37 A5X C5B H5 SING N N 38 A5X C5A H6 SING N N 39 A5X C5A H7 SING N N 40 A5X C4A H8 SING N N 41 A5X C4A H9 SING N N 42 A5X C4A H10 SING N N 43 A5X O31 H12 SING N N 44 A5X C22 H13 SING N N 45 A5X C22 H14 SING N N 46 A5X C22 H15 SING N N 47 A5X O24 H16 SING N N 48 A5X C35 H17 SING N N 49 A5X C35 H18 SING N N 50 A5X "C6'" H19 SING N N 51 A5X C2A H20 SING N N 52 A5X C2A H21 SING N N 53 A5X C2A H22 SING N N 54 A5X "N4'" H23 SING N N 55 A5X "N4'" H24 SING N N 56 A5X P3 H25 SING N N 57 # 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 A5X SMILES ACDLabs 12.01 "OP(=O)(O)OP(OCCc1c([n+](c(s1)C(P(O)=O)(C)O)Cc2cnc(nc2N)C)C)(O)=O" A5X InChI InChI 1.03 "InChI=1S/C14H23N4O10P3S/c1-8-11(4-5-27-31(25,26)28-30(22,23)24)32-13(14(3,19)29(20)21)18(8)7-10-6-16-9(2)17-12(10)15/h6,19,29H,4-5,7H2,1-3H3,(H5-,15,16,17,20,21,22,23,24,25,26)/p+1/t14-/m0/s1" A5X InChIKey InChI 1.03 CAOFPOCACDCAFN-AWEZNQCLSA-O A5X SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C@@](C)(O)[PH](O)=O)c(N)n1" A5X SMILES CACTVS 3.385 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C](C)(O)[PH](O)=O)c(N)n1" A5X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](C)(O)P(=O)O)CCOP(=O)(O)OP(=O)(O)O" A5X SMILES "OpenEye OEToolkits" 2.0.6 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(C)(O)P(=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 A5X "SYSTEMATIC NAME" ACDLabs 12.01 "3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(1S)-1-hydroxy-1-[(R)-hydroxy(oxo)-lambda~5~-phosphanyl]ethyl}-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium" A5X "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(1~{S})-1-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-1-oxidanyl-ethyl]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 A5X "Create component" 2018-02-19 RCSB A5X "Modify formal charge" 2018-02-19 RCSB A5X "Initial release" 2018-07-11 RCSB #