data_X4M
#

_chem_comp.id                                   X4M
_chem_comp.name                                 "(2R,5R,7R,8R,10R,12aR,14R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-16-hydroxy-14-[(pyrimidin-4-yl)oxy]-2,10-disulfanyldecahydro-2H,10H-5,8-methano-2lambda~5~,10lambda~5~-cyclopenta[l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecine-2,10-dione"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C20 H25 N7 O10 P2 S2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-11-30
_chem_comp.pdbx_modified_date                   2021-05-28
_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                       649.531
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    X4M
_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       7KW1
_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
X4M  C4   C1   C  0  1  Y  N  N  40.837   7.895  19.412   1.977   0.183  -2.765  C4   X4M   1  
X4M  C5   C2   C  0  1  Y  N  N  39.551   9.458  18.796   1.914   2.341  -2.575  C5   X4M   2  
X4M  C6   C3   C  0  1  Y  N  N  45.929   9.401  16.912  -5.656   1.383   0.579  C6   X4M   3  
X4M  C7   C4   C  0  1  Y  N  N  38.899   8.297  18.443   2.713   1.857  -1.533  C7   X4M   4  
X4M  C8   C5   C  0  1  N  N  N  38.919  10.712  18.509   1.709   3.737  -2.678  C8   X4M   5  
X4M  C10  C6   C  0  1  N  N  N  45.556   5.908  15.744  -2.739   0.087   2.287  C10  X4M   6  
X4M  C13  C7   C  0  1  N  N  N  41.698   4.222  20.784   1.884  -3.254  -1.699  C13  X4M   7  
X4M  C15  C8   C  0  1  N  N  S  44.703   5.845  17.918  -1.860  -1.003   0.248  C15  X4M   8  
X4M  C17  C9   C  0  1  N  N  R  40.704   5.297  17.875   2.573  -0.800   0.408  C17  X4M   9  
X4M  C20  C10  C  0  1  N  N  R  39.586   5.860  18.704   3.444  -0.453  -0.811  C20  X4M  10  
X4M  C1   C11  C  0  1  Y  N  N  45.185  10.533  16.690  -6.184   2.619   0.206  C1   X4M  11  
X4M  C2   C12  C  0  1  Y  N  N  45.675  11.736  17.153  -7.521   2.686  -0.135  C2   X4M  12  
X4M  C3   C13  C  0  1  Y  N  N  47.545  10.651  17.993  -7.725   0.430   0.262  C3   X4M  13  
X4M  C9   C14  C  0  1  N  N  N  37.113   9.306  17.567   3.066   4.009  -0.773  C9   X4M  14  
X4M  C11  C15  C  0  1  N  N  N  46.083   6.435  17.995  -3.359  -0.763   0.041  C11  X4M  15  
X4M  C12  C16  C  0  1  N  N  N  43.411   4.656  16.179  -0.305   0.288   1.729  C12  X4M  16  
X4M  C14  C17  C  0  1  N  N  R  44.789   5.003  16.691  -1.524  -0.635   1.696  C14  X4M  17  
X4M  C16  C18  C  0  1  N  N  R  40.499   4.044  19.866   3.102  -2.792  -0.894  C16  X4M  18  
X4M  C18  C19  C  0  1  N  N  R  46.238   6.976  16.596  -3.886  -0.035   1.281  C18  X4M  19  
X4M  C19  C20  C  0  1  N  N  R  40.869   3.909  18.419   2.640  -2.342   0.507  C19  X4M  20  
X4M  N21  N1   N  0  1  Y  N  N  46.849  11.772  17.792  -8.254   1.582  -0.096  N21  X4M  21  
X4M  N22  N2   N  0  1  Y  N  N  47.096   9.471  17.556  -6.454   0.322   0.594  N22  X4M  22  
X4M  N23  N3   N  0  1  Y  N  N  40.754   9.206  19.403   1.494   1.270  -3.291  N23  X4M  23  
X4M  N24  N4   N  0  1  N  N  N  37.695   8.179  17.828   3.263   2.714  -0.665  N24  X4M  24  
X4M  N25  N5   N  0  1  Y  N  N  39.750   7.294  18.841   2.735   0.495  -1.673  N25  X4M  25  
X4M  N26  N6   N  0  1  N  N  N  37.703  10.509  17.894   2.298   4.541  -1.765  N26  X4M  26  
X4M  N27  N7   N  0  1  N  N  N  35.885   9.431  16.954   3.651   4.850   0.140  N27  X4M  27  
X4M  O28  O1   O  0  1  N  N  N  39.407  11.804  18.789   1.020   4.203  -3.569  O28  X4M  28  
X4M  S29  S1   S  0  1  N  N  N  40.922   5.220  13.647   2.962  -0.187   4.652  S29  X4M  29  
X4M  S30  S2   S  0  1  N  N  N  44.895   4.119  21.763  -1.735  -4.527  -2.161  S30  X4M  30  
X4M  O31  O2   O  0  1  N  N  N  42.778   5.893  15.896   0.676  -0.248   2.618  O31  X4M  31  
X4M  O32  O3   O  0  1  N  N  N  42.476   5.322  20.375   0.749  -3.332  -0.833  O32  X4M  32  
X4M  O33  O4   O  0  1  N  N  N  39.668   5.202  19.968   3.701  -1.661  -1.529  O33  X4M  33  
X4M  O34  O5   O  0  1  N  N  N  44.547   4.945  19.002  -1.552  -2.378   0.011  O34  X4M  34  
X4M  O35  O6   O  0  1  N  N  N  40.331   5.217  16.502   3.097  -0.205   1.594  O35  X4M  35  
X4M  O36  O7   O  0  1  N  N  N  39.860   3.102  17.810   3.590  -2.738   1.498  O36  X4M  36  
X4M  O37  O8   O  0  1  N  N  N  40.871   7.581  15.552   2.090   1.842   2.677  O37  X4M  37  
X4M  O38  O9   O  0  1  N  N  N  44.375   6.958  20.618  -0.633  -1.778  -2.263  O38  X4M  38  
X4M  O39  O10  O  0  1  N  N  N  45.472   8.181  16.453  -4.349   1.267   0.916  O39  X4M  39  
X4M  P40  P1   P  0  1  N  N  R  41.219   6.007  15.404   2.156   0.367   2.770  P40  X4M  40  
X4M  P41  P2   P  0  1  N  N  R  44.106   5.370  20.499  -0.730  -2.881  -1.280  P41  X4M  41  
X4M  H1   H1   H  0  1  N  N  N  41.673   7.351  19.826   1.802  -0.817  -3.133  H1   X4M  42  
X4M  H2   H2   H  0  1  N  N  N  44.865   6.380  15.030  -3.023  -0.380   3.230  H2   X4M  43  
X4M  H3   H3   H  0  1  N  N  N  46.310   5.326  15.194  -2.501   1.138   2.451  H3   X4M  44  
X4M  H4   H4   H  0  1  N  N  N  41.344   4.391  21.812   1.684  -2.540  -2.498  H4   X4M  45  
X4M  H5   H5   H  0  1  N  N  N  42.315   3.312  20.754   2.082  -4.236  -2.129  H5   X4M  46  
X4M  H6   H6   H  0  1  N  N  N  43.917   6.612  17.855  -1.289  -0.375  -0.436  H6   X4M  47  
X4M  H7   H7   H  0  1  N  N  N  41.625   5.882  18.016   1.546  -0.481   0.244  H7   X4M  48  
X4M  H8   H8   H  0  1  N  N  N  38.625   5.636  18.218   4.386  -0.016  -0.479  H8   X4M  49  
X4M  H9   H9   H  0  1  N  N  N  44.241  10.483  16.167  -5.562   3.502   0.183  H9   X4M  50  
X4M  H10  H10  H  0  1  N  N  N  45.113  12.645  17.000  -7.964   3.626  -0.429  H10  X4M  51  
X4M  H11  H11  H  0  1  N  N  N  48.488  10.699  18.518  -8.349  -0.451   0.284  H11  X4M  52  
X4M  H12  H12  H  0  1  N  N  N  46.839   5.668  18.218  -3.515  -0.146  -0.844  H12  X4M  53  
X4M  H13  H13  H  0  1  N  N  N  46.139   7.236  18.747  -3.873  -1.716  -0.077  H13  X4M  54  
X4M  H14  H14  H  0  1  N  N  N  42.846   4.104  16.945   0.117   0.368   0.728  H14  X4M  55  
X4M  H15  H15  H  0  1  N  N  N  43.484   4.046  15.266  -0.608   1.276   2.076  H15  X4M  56  
X4M  H16  H16  H  0  1  N  N  N  45.364   4.087  16.890  -1.322  -1.539   2.269  H16  X4M  57  
X4M  H17  H17  H  0  1  N  N  N  39.941   3.150  20.180   3.821  -3.603  -0.805  H17  X4M  58  
X4M  H18  H18  H  0  1  N  N  N  47.295   7.101  16.319  -4.704  -0.605   1.722  H18  X4M  59  
X4M  H19  H19  H  0  1  N  N  N  41.889   3.521  18.280   1.656  -2.752   0.734  H19  X4M  60  
X4M  H20  H20  H  0  1  N  N  N  37.187  11.332  17.656   2.173   5.502  -1.816  H20  X4M  61  
X4M  H21  H21  H  0  1  N  N  N  35.379   8.614  16.677   4.200   4.486   0.853  H21  X4M  62  
X4M  H22  H22  H  0  1  N  N  N  35.500  10.339  16.786   3.516   5.808   0.074  H22  X4M  63  
X4M  H23  H23  H  0  1  N  N  N  41.281   3.986  13.840   2.088   0.347   5.524  H23  X4M  64  
X4M  H24  H24  H  0  1  N  N  N  44.463   4.576  22.901  -0.950  -4.835  -3.208  H24  X4M  65  
X4M  H25  H25  H  0  1  N  N  N  39.931   2.210  18.130   3.673  -3.696   1.602  H25  X4M  66  
#   #
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
X4M  S29  P40  SING  N  N   1  
X4M  P40  O37  DOUB  N  N   2  
X4M  P40  O31  SING  N  N   3  
X4M  P40  O35  SING  N  N   4  
X4M  C10  C18  SING  N  N   5  
X4M  C10  C14  SING  N  N   6  
X4M  O31  C12  SING  N  N   7  
X4M  C12  C14  SING  N  N   8  
X4M  O39  C18  SING  N  N   9  
X4M  O39  C6   SING  N  N  10  
X4M  O35  C17  SING  N  N  11  
X4M  C18  C11  SING  N  N  12  
X4M  C1   C6   SING  Y  N  13  
X4M  C1   C2   DOUB  Y  N  14  
X4M  C14  C15  SING  N  N  15  
X4M  C6   N22  DOUB  Y  N  16  
X4M  N27  C9   SING  N  N  17  
X4M  C2   N21  SING  Y  N  18  
X4M  N22  C3   SING  Y  N  19  
X4M  C9   N24  DOUB  N  N  20  
X4M  C9   N26  SING  N  N  21  
X4M  N21  C3   DOUB  Y  N  22  
X4M  O36  C19  SING  N  N  23  
X4M  N24  C7   SING  N  N  24  
X4M  C17  C19  SING  N  N  25  
X4M  C17  C20  SING  N  N  26  
X4M  N26  C8   SING  N  N  27  
X4M  C15  C11  SING  N  N  28  
X4M  C15  O34  SING  N  N  29  
X4M  C19  C16  SING  N  N  30  
X4M  C7   C5   DOUB  Y  N  31  
X4M  C7   N25  SING  Y  N  32  
X4M  C8   O28  DOUB  N  N  33  
X4M  C8   C5   SING  N  N  34  
X4M  C20  N25  SING  N  N  35  
X4M  C20  O33  SING  N  N  36  
X4M  C5   N23  SING  Y  N  37  
X4M  N25  C4   SING  Y  N  38  
X4M  O34  P41  SING  N  N  39  
X4M  N23  C4   DOUB  Y  N  40  
X4M  C16  O33  SING  N  N  41  
X4M  C16  C13  SING  N  N  42  
X4M  O32  P41  SING  N  N  43  
X4M  O32  C13  SING  N  N  44  
X4M  P41  O38  DOUB  N  N  45  
X4M  P41  S30  SING  N  N  46  
X4M  C4   H1   SING  N  N  47  
X4M  C10  H2   SING  N  N  48  
X4M  C10  H3   SING  N  N  49  
X4M  C13  H4   SING  N  N  50  
X4M  C13  H5   SING  N  N  51  
X4M  C15  H6   SING  N  N  52  
X4M  C17  H7   SING  N  N  53  
X4M  C20  H8   SING  N  N  54  
X4M  C1   H9   SING  N  N  55  
X4M  C2   H10  SING  N  N  56  
X4M  C3   H11  SING  N  N  57  
X4M  C11  H12  SING  N  N  58  
X4M  C11  H13  SING  N  N  59  
X4M  C12  H14  SING  N  N  60  
X4M  C12  H15  SING  N  N  61  
X4M  C14  H16  SING  N  N  62  
X4M  C16  H17  SING  N  N  63  
X4M  C18  H18  SING  N  N  64  
X4M  C19  H19  SING  N  N  65  
X4M  N26  H20  SING  N  N  66  
X4M  N27  H21  SING  N  N  67  
X4M  N27  H22  SING  N  N  68  
X4M  S29  H23  SING  N  N  69  
X4M  S30  H24  SING  N  N  70  
X4M  O36  H25  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
X4M  SMILES            ACDLabs               12.01  "c1nc6c(n1C5C3C(C(COP(S)(OC2CC(CC2COP(S)(O3)=O)Oc4ncncc4)=O)O5)O)N=C(NC6=O)N"  
X4M  InChI             InChI                 1.03   "InChI=1S/C20H25N7O10P2S2/c21-20-25-17-14(18(29)26-20)24-8-27(17)19-16-15(28)12(35-19)6-33-38(30,40)36-11-4-10(34-13-1-2-22-7-23-13)3-9(11)5-32-39(31,41)37-16/h1-2,7-12,15-16,19,28H,3-6H2,(H,30,40)(H,31,41)(H3,21,25,26,29)/t9-,10-,11+,12-,15-,16-,19-,38-,39-/m1/s1"  
X4M  InChIKey          InChI                 1.03   OYKBZTYSLUEHAP-FEFYGENMSA-N  
X4M  SMILES_CANONICAL  CACTVS                3.385  "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@@H]4CO[P@](S)(=O)O[C@H]5C[C@@H](C[C@@H]5CO[P@](S)(=O)O[C@@H]3[C@@H]4O)Oc6ccncn6"  
X4M  SMILES            CACTVS                3.385  "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH]4CO[P](S)(=O)O[CH]5C[CH](C[CH]5CO[P](S)(=O)O[CH]3[CH]4O)Oc6ccncn6"  
X4M  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1cncnc1O[C@@H]2C[C@@H]3CO[P@](=O)(O[C@@H]4[C@@H]([C@@H](CO[P@](=O)(O[C@H]3C2)S)O[C@H]4n5cnc6c5N=C(NC6=O)N)O)S"  
X4M  SMILES            "OpenEye OEToolkits"  2.0.7  "c1cncnc1OC2CC3COP(=O)(OC4C(C(COP(=O)(OC3C2)S)OC4n5cnc6c5N=C(NC6=O)N)O)S"  
#   #
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
X4M  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2R,5R,7R,8R,10R,12aR,14R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-16-hydroxy-14-[(pyrimidin-4-yl)oxy]-2,10-disulfanyldecahydro-2H,10H-5,8-methano-2lambda~5~,10lambda~5~-cyclopenta[l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecine-2,10-dione"  
X4M  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "2-azanyl-9-[(1~{R},3~{R},6~{R},8~{R},10~{S},12~{R},15~{R},17~{R},18~{R})-18-oxidanyl-3,12-bis(oxidanylidene)-8-pyrimidin-4-yloxy-3,12-bis(sulfanyl)-2,4,11,13,16-pentaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-1~{H}-purin-6-one"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
X4M  "Create component"  2020-11-30  RCSB  
X4M  "Initial release"   2021-06-02  RCSB  
##
