data_9XR
#

_chem_comp.id                                   9XR
_chem_comp.name                                 "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylanilino)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C22 H29 N7 O14 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-11-01
_chem_comp.pdbx_modified_date                   2022-04-08
_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                       677.452
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    9XR
_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       7SNE
_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
9XR  O7N   O1   O  0  1  N  N  N   -2.951  56.542  21.053  -7.658  -2.933   1.185  O7N   9XR   1  
9XR  C7N   C1   C  0  1  N  N  N   -4.058  56.037  20.827  -7.814  -3.447   0.095  C7N   9XR   2  
9XR  N7N   N1   N  0  1  N  N  N   -5.177  56.719  21.017  -8.223  -4.728   0.006  N7N   9XR   3  
9XR  C3N   C2   C  0  1  Y  N  N   -4.086  54.627  20.339  -7.561  -2.664  -1.134  C3N   9XR   4  
9XR  C2N   C3   C  0  1  Y  N  N   -5.154  54.152  19.584  -7.133  -1.340  -1.045  C2N   9XR   5  
9XR  C4N   C4   C  0  1  Y  N  N   -3.027  53.794  20.658  -7.745  -3.251  -2.388  C4N   9XR   6  
9XR  C5N   C5   C  0  1  Y  N  N   -3.019  52.489  20.208  -7.508  -2.519  -3.533  C5N   9XR   7  
9XR  C6N   C6   C  0  1  Y  N  N   -4.072  52.015  19.432  -7.089  -1.204  -3.445  C6N   9XR   8  
9XR  C1N   C7   C  0  1  Y  N  N   -5.130  52.859  19.106  -6.893  -0.615  -2.202  C1N   9XR   9  
9XR  C1D   C8   C  0  1  N  N  S   -7.516  52.886  18.484  -6.405   1.381  -0.816  C1D   9XR  10  
9XR  O4D   O2   O  0  1  N  N  N   -7.728  53.769  17.379  -5.079   1.279  -0.282  O4D   9XR  11  
9XR  C2D   C9   C  0  1  N  N  R   -8.670  51.870  18.447  -6.728   2.882  -0.977  C2D   9XR  12  
9XR  O2D   O3   O  0  1  N  N  N   -8.303  50.563  18.072  -6.489   3.312  -2.319  O2D   9XR  13  
9XR  C3D   C10  C  0  1  N  N  S   -9.622  52.426  17.411  -5.724   3.544   0.006  C3D   9XR  14  
9XR  O3D   O4   O  0  1  N  N  N   -9.483  51.755  16.170  -5.387   4.867  -0.414  O3D   9XR  15  
9XR  C4D   C11  C  0  1  N  N  R   -9.148  53.848  17.239  -4.511   2.589  -0.126  C4D   9XR  16  
9XR  C5D   C12  C  0  1  N  N  N   -9.736  54.751  18.319  -3.650   2.647   1.137  C5D   9XR  17  
9XR  O5D   O5   O  0  1  N  N  N   -9.011  55.969  18.377  -2.510   1.800   0.976  O5D   9XR  18  
9XR  PN    P1   P  0  1  N  N  N   -8.842  56.721  19.777  -1.386   1.617   2.114  PN    9XR  19  
9XR  O1N   O6   O  0  1  N  N  N   -8.272  55.812  20.822  -0.621   3.016   2.342  O1N   9XR  20  
9XR  O2N   O7   O  0  1  N  N  N   -8.156  58.030  19.479  -2.027   1.193   3.379  O2N   9XR  21  
9XR  O3    O8   O  0  1  N  N  N  -10.385  56.988  20.076  -0.327   0.497   1.647  O3    9XR  22  
9XR  PA    P2   P  0  1  N  N  N  -11.122  57.811  21.265   0.741  -0.424   2.423  PA    9XR  23  
9XR  O1A   O9   O  0  1  N  N  N  -10.776  57.171  22.576  -0.016  -1.680   3.088  O1A   9XR  24  
9XR  O2A   O10  O  0  1  N  N  N  -12.573  57.912  20.880   1.401   0.371   3.483  O2A   9XR  25  
9XR  O5B   O11  O  0  1  N  N  N  -10.407  59.251  21.236   1.848  -0.955   1.382  O5B   9XR  26  
9XR  C5B   C13  C  0  1  N  N  N  -10.578  60.144  20.150   2.992  -1.713   1.781  C5B   9XR  27  
9XR  C4B   C14  C  0  1  N  N  R  -10.827  61.523  20.734   3.833  -2.054   0.549  C4B   9XR  28  
9XR  C3B   C15  C  0  1  N  N  S   -9.826  61.990  21.790   5.011  -2.961   0.954  C3B   9XR  29  
9XR  O3B   O12  O  0  1  N  N  N   -8.617  62.547  21.276   4.941  -4.210   0.262  O3B   9XR  30  
9XR  C2B   C16  C  0  1  N  N  R  -10.609  63.079  22.481   6.267  -2.169   0.518  C2B   9XR  31  
9XR  O2B   O13  O  0  1  N  N  N  -10.741  64.251  21.658   7.241  -3.038  -0.065  O2B   9XR  32  
9XR  C1B   C17  C  0  1  N  N  R  -11.976  62.452  22.538   5.688  -1.199  -0.542  C1B   9XR  33  
9XR  O4B   O14  O  0  1  N  N  N  -12.105  61.575  21.393   4.391  -0.853  -0.009  O4B   9XR  34  
9XR  N9A   N2   N  0  1  Y  N  N  -12.339  61.639  23.720   6.530  -0.006  -0.665  N9A   9XR  35  
9XR  C4A   C18  C  0  1  Y  N  N  -13.148  62.051  24.681   7.646   0.122  -1.452  C4A   9XR  36  
9XR  C5A   C19  C  0  1  Y  N  N  -13.332  60.884  25.535   8.118   1.429  -1.247  C5A   9XR  37  
9XR  N7A   N3   N  0  1  Y  N  N  -12.674  59.843  25.001   7.280   2.021  -0.361  N7A   9XR  38  
9XR  C8A   C20  C  0  1  Y  N  N  -12.078  60.323  23.901   6.345   1.182  -0.023  C8A   9XR  39  
9XR  N3A   N4   N  0  1  Y  N  N  -13.708  63.238  24.999   8.301  -0.677  -2.289  N3A   9XR  40  
9XR  C2A   C21  C  0  1  Y  N  N  -14.455  63.294  26.101   9.377  -0.252  -2.918  C2A   9XR  41  
9XR  N1A   N5   N  0  1  Y  N  N  -14.677  62.255  26.929   9.857   0.967  -2.757  N1A   9XR  42  
9XR  C6A   C22  C  0  1  Y  N  N  -14.161  61.040  26.716   9.270   1.836  -1.941  C6A   9XR  43  
9XR  N6A   N6   N  0  1  N  N  N  -14.381  60.025  27.554   9.781   3.112  -1.778  N6A   9XR  44  
9XR  N8N   N7   N  0  1  N  N  N   -6.193  52.309  18.430  -6.469   0.714  -2.118  N8N   9XR  45  
9XR  H71N  H1   H  0  0  N  N  N   -5.138  57.661  21.349  -8.392  -5.240   0.812  H71N  9XR  46  
9XR  H72N  H2   H  0  0  N  N  N   -6.061  56.292  20.828  -8.347  -5.138  -0.864  H72N  9XR  47  
9XR  H2N   H3   H  0  1  N  N  N   -5.997  54.793  19.374  -6.990  -0.881  -0.078  H2N   9XR  48  
9XR  H4N   H4   H  0  1  N  N  N   -2.209  54.165  21.258  -8.072  -4.277  -2.461  H4N   9XR  49  
9XR  H5N   H5   H  0  1  N  N  N   -2.196  51.836  20.458  -7.650  -2.974  -4.502  H5N   9XR  50  
9XR  H6N1  H6   H  0  0  N  N  N   -4.069  50.993  19.083  -6.904  -0.637  -4.345  H6N1  9XR  51  
9XR  H1D   H7   H  0  1  N  N  N   -7.611  53.459  19.418  -7.116   0.922  -0.129  H1D   9XR  52  
9XR  H2D   H8   H  0  1  N  N  N   -9.168  51.865  19.428  -7.756   3.092  -0.682  H2D   9XR  53  
9XR  HO2N  H9   H  0  0  N  N  N   -7.705  50.204  18.717  -7.034   2.862  -2.979  HO2N  9XR  54  
9XR  H3D   H10  H  0  1  N  N  N  -10.657  52.402  17.782  -6.114   3.545   1.024  H3D   9XR  55  
9XR  HO3N  H11  H  0  0  N  N  N   -9.778  50.856  16.261  -6.141   5.472  -0.450  HO3N  9XR  56  
9XR  H4D   H12  H  0  1  N  N  N   -9.430  54.223  16.244  -3.917   2.851  -1.002  H4D   9XR  57  
9XR  H51N  H13  H  0  0  N  N  N  -10.789  54.964  18.083  -3.319   3.672   1.305  H51N  9XR  58  
9XR  H52N  H14  H  0  0  N  N  N   -9.674  54.243  19.293  -4.235   2.310   1.992  H52N  9XR  59  
9XR  H1    H15  H  0  1  N  N  N   -7.491  56.206  21.193  -0.177   3.354   1.553  H1    9XR  60  
9XR  H2    H16  H  0  1  N  N  N  -11.573  56.898  23.015  -0.472  -2.247   2.451  H2    9XR  61  
9XR  H52A  H17  H  0  0  N  N  N  -11.438  59.833  19.539   3.590  -1.128   2.479  H52A  9XR  62  
9XR  H51A  H18  H  0  0  N  N  N   -9.671  60.157  19.527   2.667  -2.634   2.265  H51A  9XR  63  
9XR  H4B   H19  H  0  1  N  N  N  -10.816  62.251  19.909   3.214  -2.556  -0.195  H4B   9XR  64  
9XR  H3B   H20  H  0  1  N  N  N   -9.619  61.171  22.494   5.016  -3.122   2.032  H3B   9XR  65  
9XR  HO3A  H21  H  0  0  N  N  N   -8.057  62.809  21.997   5.659  -4.820   0.479  HO3A  9XR  66  
9XR  H2B   H22  H  0  1  N  N  N  -10.213  63.298  23.484   6.692  -1.620   1.358  H2B   9XR  67  
9XR  HO2A  H23  H  0  0  N  N  N  -11.238  64.912  22.125   7.568  -3.722   0.536  HO2A  9XR  68  
9XR  H1B   H24  H  0  1  N  N  N  -12.717  63.259  22.441   5.588  -1.698  -1.506  H1B   9XR  69  
9XR  H8A   H25  H  0  1  N  N  N  -11.463  59.731  23.239   5.541   1.395   0.667  H8A   9XR  70  
9XR  H2A   H26  H  0  1  N  N  N  -14.915  64.239  26.348   9.885  -0.926  -3.591  H2A   9XR  71  
9XR  H61A  H27  H  0  0  N  N  N  -14.961  60.334  28.308   9.344   3.737  -1.179  H61A  9XR  72  
9XR  H62A  H28  H  0  0  N  N  N  -14.838  59.282  27.065  10.577   3.381  -2.263  H62A  9XR  73  
9XR  HN8N  H29  H  0  0  N  N  N   -6.283  51.371  18.765  -6.218   1.195  -2.922  HN8N  9XR  74  
#   #
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
9XR  O3D  C3D   SING  N  N   1  
9XR  C4D  O4D   SING  N  N   2  
9XR  C4D  C3D   SING  N  N   3  
9XR  C4D  C5D   SING  N  N   4  
9XR  O4D  C1D   SING  N  N   5  
9XR  C3D  C2D   SING  N  N   6  
9XR  O2D  C2D   SING  N  N   7  
9XR  C5D  O5D   SING  N  N   8  
9XR  O5D  PN    SING  N  N   9  
9XR  N8N  C1D   SING  N  N  10  
9XR  N8N  C1N   SING  N  N  11  
9XR  C2D  C1D   SING  N  N  12  
9XR  C1N  C6N   DOUB  Y  N  13  
9XR  C1N  C2N   SING  Y  N  14  
9XR  C6N  C5N   SING  Y  N  15  
9XR  O2N  PN    DOUB  N  N  16  
9XR  C2N  C3N   DOUB  Y  N  17  
9XR  PN   O3    SING  N  N  18  
9XR  PN   O1N   SING  N  N  19  
9XR  O3   PA    SING  N  N  20  
9XR  C5B  C4B   SING  N  N  21  
9XR  C5B  O5B   SING  N  N  22  
9XR  C5N  C4N   DOUB  Y  N  23  
9XR  C3N  C4N   SING  Y  N  24  
9XR  C3N  C7N   SING  N  N  25  
9XR  C4B  O4B   SING  N  N  26  
9XR  C4B  C3B   SING  N  N  27  
9XR  C7N  N7N   SING  N  N  28  
9XR  C7N  O7N   DOUB  N  N  29  
9XR  O2A  PA    DOUB  N  N  30  
9XR  O5B  PA    SING  N  N  31  
9XR  PA   O1A   SING  N  N  32  
9XR  O3B  C3B   SING  N  N  33  
9XR  O4B  C1B   SING  N  N  34  
9XR  O2B  C2B   SING  N  N  35  
9XR  C3B  C2B   SING  N  N  36  
9XR  C2B  C1B   SING  N  N  37  
9XR  C1B  N9A   SING  N  N  38  
9XR  N9A  C8A   SING  Y  N  39  
9XR  N9A  C4A   SING  Y  N  40  
9XR  C8A  N7A   DOUB  Y  N  41  
9XR  C4A  N3A   DOUB  Y  N  42  
9XR  C4A  C5A   SING  Y  N  43  
9XR  N3A  C2A   SING  Y  N  44  
9XR  N7A  C5A   SING  Y  N  45  
9XR  C5A  C6A   DOUB  Y  N  46  
9XR  C2A  N1A   DOUB  Y  N  47  
9XR  C6A  N1A   SING  Y  N  48  
9XR  C6A  N6A   SING  N  N  49  
9XR  N7N  H71N  SING  N  N  50  
9XR  N7N  H72N  SING  N  N  51  
9XR  C2N  H2N   SING  N  N  52  
9XR  C4N  H4N   SING  N  N  53  
9XR  C5N  H5N   SING  N  N  54  
9XR  C6N  H6N1  SING  N  N  55  
9XR  C1D  H1D   SING  N  N  56  
9XR  C2D  H2D   SING  N  N  57  
9XR  O2D  HO2N  SING  N  N  58  
9XR  C3D  H3D   SING  N  N  59  
9XR  O3D  HO3N  SING  N  N  60  
9XR  C4D  H4D   SING  N  N  61  
9XR  C5D  H51N  SING  N  N  62  
9XR  C5D  H52N  SING  N  N  63  
9XR  O1N  H1    SING  N  N  64  
9XR  O1A  H2    SING  N  N  65  
9XR  C5B  H52A  SING  N  N  66  
9XR  C5B  H51A  SING  N  N  67  
9XR  C4B  H4B   SING  N  N  68  
9XR  C3B  H3B   SING  N  N  69  
9XR  O3B  HO3A  SING  N  N  70  
9XR  C2B  H2B   SING  N  N  71  
9XR  O2B  HO2A  SING  N  N  72  
9XR  C1B  H1B   SING  N  N  73  
9XR  C8A  H8A   SING  N  N  74  
9XR  C2A  H2A   SING  N  N  75  
9XR  N6A  H61A  SING  N  N  76  
9XR  N6A  H62A  SING  N  N  77  
9XR  N8N  HN8N  SING  N  N  78  
#   #
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
9XR  SMILES            ACDLabs               12.01  "NC(=O)c1cc(ccc1)NC1OC(COP(=O)(O)OP(=O)(O)OCC2OC(n3cnc4c(N)ncnc43)C(O)C2O)C(O)C1O"  
9XR  InChI             InChI                 1.03   "InChI=1S/C22H29N7O14P2/c23-18-13-20(26-7-25-18)29(8-27-13)22-17(33)15(31)12(42-22)6-40-45(37,38)43-44(35,36)39-5-11-14(30)16(32)21(41-11)28-10-3-1-2-9(4-10)19(24)34/h1-4,7-8,11-12,14-17,21-22,28,30-33H,5-6H2,(H2,24,34)(H,35,36)(H,37,38)(H2,23,25,26)/t11-,12-,14-,15-,16-,17-,21+,22-/m1/s1"  
9XR  InChIKey          InChI                 1.03   OJEGJAIQKNCBOQ-ZLPBMXMUSA-N  
9XR  SMILES_CANONICAL  CACTVS                3.385  "NC(=O)c1cccc(N[C@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O)c1"  
9XR  SMILES            CACTVS                3.385  "NC(=O)c1cccc(N[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O)c1"  
9XR  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1cc(cc(c1)N[C@@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N"  
9XR  SMILES            "OpenEye OEToolkits"  2.0.7  "c1cc(cc(c1)NC2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N"  
#   #
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
9XR  "SYSTEMATIC NAME"  ACDLabs               12.01  "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylanilino)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)"  
9XR  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[[(2~{R},3~{S},4~{R},5~{S})-5-[(3-aminocarbonylphenyl)amino]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate"  
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loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
9XR  "Create component"  2021-11-01  RCSB  
9XR  "Initial release"   2022-04-13  RCSB  
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