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 
# 
