data_X5J
#

_chem_comp.id                                   X5J
_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)amino]-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 H26 N8 O9 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                       648.546
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    X5J
_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       7KVX
_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
X5J  C4   C1   C  0  1  Y  N  N  41.104   7.974  19.433    5.009  -2.185  -0.199  C4   X5J   1  
X5J  C5   C2   C  0  1  Y  N  N  39.626   9.322  18.684    6.755  -0.919  -0.413  C5   X5J   2  
X5J  C6   C3   C  0  1  Y  N  N  45.906   9.223  16.679   -7.354   1.111  -0.236  C6   X5J   3  
X5J  C7   C4   C  0  1  Y  N  N  39.115   8.061  18.490    5.754  -0.147   0.189  C7   X5J   4  
X5J  C8   C5   C  0  1  N  N  N  38.823  10.453  18.269    8.011  -0.320  -0.668  C8   X5J   5  
X5J  C10  C6   C  0  1  N  N  N  45.816   5.660  15.777   -3.994   1.769   1.209  C10  X5J   6  
X5J  C13  C7   C  0  1  N  N  N  42.136   4.016  20.770    0.850  -3.131   0.529  C13  X5J   7  
X5J  C15  C8   C  0  1  N  N  R  46.288   6.879  16.539   -5.159   0.837   0.859  C15  X5J   8  
X5J  C17  C9   C  0  1  N  N  R  40.786   3.905  20.113    1.322  -1.739   0.950  C17  X5J   9  
X5J  C20  C10  C  0  1  N  N  R  39.929   5.743  18.960    3.368  -0.603   0.885  C20  X5J  10  
X5J  C1   C11  C  0  1  Y  N  N  45.155  10.354  16.459   -7.889   0.141   0.614  C1   X5J  11  
X5J  C2   C12  C  0  1  Y  N  N  45.673  11.561  16.870   -9.224  -0.184   0.480  C2   X5J  12  
X5J  C3   C13  C  0  1  Y  N  N  47.508  10.520  17.635   -9.416   1.344  -1.230  C3   X5J  13  
X5J  C9   C14  C  0  1  N  N  N  37.194   8.683  17.556    7.176   1.671   0.271  C9   X5J  14  
X5J  C11  C15  C  0  1  N  N  N  46.153   6.445  17.973   -4.580  -0.461   0.286  C11  X5J  15  
X5J  C12  C16  C  0  1  N  N  N  43.576   4.534  16.162   -1.756   1.855   0.080  C12  X5J  16  
X5J  C14  C17  C  0  1  N  N  R  44.922   4.876  16.725   -2.694   1.003   0.937  C14  X5J  17  
X5J  C16  C18  C  0  1  N  N  S  44.846   5.707  17.968   -3.060  -0.284   0.191  C16  X5J  18  
X5J  C18  C19  C  0  1  N  N  R  40.865   4.975  18.059    2.499   0.072  -0.185  C18  X5J  19  
X5J  C19  C20  C  0  1  N  N  R  40.889   3.574  18.657    1.210  -0.772  -0.243  C19  X5J  20  
X5J  N21  N1   N  0  1  Y  N  N  46.861  11.681  17.466   -9.950   0.432  -0.443  N21  X5J  21  
X5J  N22  N2   N  0  1  Y  N  N  47.101   9.294  17.273   -8.147   1.684  -1.137  N22  X5J  22  
X5J  N23  N3   N  0  1  Y  N  N  40.861   9.259  19.274    6.237  -2.154  -0.626  N23  X5J  23  
X5J  N24  N4   N  0  1  N  N  N  37.935   7.700  17.943    6.004   1.127   0.510  N24  X5J  24  
X5J  N25  N5   N  0  1  Y  N  N  40.068   7.199  18.967    4.665  -0.967   0.310  N25  X5J  25  
X5J  N26  N6   N  0  1  N  N  N  37.608  10.003  17.710    8.189   0.972  -0.315  N26  X5J  26  
X5J  N27  N7   N  0  1  N  N  N  35.990   8.442  16.983    7.385   2.982   0.618  N27  X5J  27  
X5J  N28  N8   N  0  1  N  N  N  45.380   7.991  16.255   -6.021   1.476  -0.138  N28  X5J  28  
X5J  O29  O1   O  0  1  N  N  N  39.200  11.623  18.415    8.911  -0.954  -1.192  O29  X5J  29  
X5J  O30  O2   O  0  1  N  N  N  40.892   7.151  15.207    0.658   1.922  -1.740  O30  X5J  30  
X5J  O31  O3   O  0  1  N  N  N  44.818   6.797  20.973   -1.097  -1.990  -1.283  O31  X5J  31  
X5J  O32  O4   O  0  1  N  N  N  42.855   5.743  16.028   -0.411   1.677   0.531  O32  X5J  32  
X5J  O33  O5   O  0  1  N  N  N  42.727   5.291  20.635   -0.543  -3.262   0.826  O33  X5J  33  
X5J  O34  O6   O  0  1  N  N  N  40.067   5.139  20.230    2.696  -1.780   1.341  O34  X5J  34  
X5J  O35  O7   O  0  1  N  N  N  44.788   4.896  19.126   -2.401  -1.398   0.795  O35  X5J  35  
X5J  O36  O8   O  0  1  N  N  N  40.426   5.047  16.716    2.189   1.413   0.199  O36  X5J  36  
X5J  O37  O9   O  0  1  N  N  N  39.798   2.709  18.264    0.060   0.064  -0.100  O37  X5J  37  
X5J  P38  P1   P  0  1  N  N  R  41.309   5.743  15.523    0.869   2.188  -0.299  P38  X5J  38  
X5J  P39  P2   P  0  1  N  N  R  44.352   5.408  20.621   -1.696  -2.567  -0.058  P39  X5J  39  
X5J  S40  S1   S  0  1  N  N  N  41.082   4.440  13.906    1.121   4.271   0.003  S40  X5J  40  
X5J  S41  S2   S  0  1  N  N  N  45.165   3.940  21.864   -3.143  -4.019  -0.598  S41  X5J  41  
X5J  H1   H1   H  0  1  N  N  N  42.006   7.578  19.875    4.358  -3.045  -0.245  H1   X5J  42  
X5J  H2   H2   H  0  1  N  N  N  45.249   5.966  14.885   -4.035   2.662   0.585  H2   X5J  43  
X5J  H3   H3   H  0  1  N  N  N  46.676   5.046  15.472   -4.046   2.048   2.261  H3   X5J  44  
X5J  H4   H4   H  0  1  N  N  N  42.020   3.798  21.842    1.009  -3.262  -0.541  H4   X5J  45  
X5J  H5   H5   H  0  1  N  N  N  42.806   3.272  20.315    1.411  -3.889   1.076  H5   X5J  46  
X5J  H6   H6   H  0  1  N  N  N  47.331   7.125  16.291   -5.736   0.617   1.757  H6   X5J  47  
X5J  H7   H7   H  0  1  N  N  N  40.221   3.105  20.614    0.711  -1.377   1.776  H7   X5J  48  
X5J  H8   H8   H  0  1  N  N  N  38.912   5.524  18.603    3.515   0.082   1.720  H8   X5J  49  
X5J  H9   H9   H  0  1  N  N  N  44.189  10.297  15.979   -7.273  -0.345   1.356  H9   X5J  50  
X5J  H10  H10  H  0  1  N  N  N  45.090  12.454  16.702   -9.672  -0.930   1.120  H10  X5J  51  
X5J  H11  H11  H  0  1  N  N  N  48.471  10.578  18.120  -10.036   1.826  -1.971  H11  X5J  52  
X5J  H12  H12  H  0  1  N  N  N  46.981   5.784  18.268   -4.815  -1.294   0.948  H12  X5J  53  
X5J  H13  H13  H  0  1  N  N  N  46.117   7.312  18.649   -4.996  -0.646  -0.704  H13  X5J  54  
X5J  H14  H14  H  0  1  N  N  N  43.045   3.853  16.844   -1.834   1.545  -0.962  H14  X5J  55  
X5J  H15  H15  H  0  1  N  N  N  43.690   4.053  15.179   -2.035   2.905   0.170  H15  X5J  56  
X5J  H16  H16  H  0  1  N  N  N  45.437   3.936  16.973   -2.210   0.758   1.881  H16  X5J  57  
X5J  H17  H17  H  0  1  N  N  N  44.002   6.411  17.915   -2.768  -0.199  -0.855  H17  X5J  58  
X5J  H18  H18  H  0  1  N  N  N  41.872   5.408  18.148    3.004   0.056  -1.149  H18  X5J  59  
X5J  H19  H19  H  0  1  N  N  N  41.858   3.099  18.447    1.161  -1.328  -1.179  H19  X5J  60  
X5J  H20  H20  H  0  1  N  N  N  36.976  10.709  17.390    9.042   1.404  -0.477  H20  X5J  61  
X5J  H21  H21  H  0  1  N  N  N  35.674   7.501  16.859    8.245   3.398   0.446  H21  X5J  62  
X5J  H22  H22  H  0  1  N  N  N  35.417   9.205  16.684    6.674   3.493   1.036  H22  X5J  63  
X5J  H23  H23  H  0  1  N  N  N  45.218   8.032  15.269   -5.659   2.154  -0.730  H23  X5J  64  
X5J  H24  H24  H  0  1  N  N  N  39.897   1.863  18.684   -0.780  -0.414  -0.128  H24  X5J  65  
X5J  H25  H25  H  0  1  N  N  N  41.495   3.314  14.407   -0.035   4.785  -0.454  H25  X5J  66  
X5J  H26  H26  H  0  1  N  N  N  44.812   4.358  23.043   -2.424  -4.918  -1.293  H26  X5J  67  
#   #
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
X5J  S40  P38  SING  N  N   1  
X5J  O30  P38  DOUB  N  N   2  
X5J  P38  O32  SING  N  N   3  
X5J  P38  O36  SING  N  N   4  
X5J  C10  C15  SING  N  N   5  
X5J  C10  C14  SING  N  N   6  
X5J  O32  C12  SING  N  N   7  
X5J  C12  C14  SING  N  N   8  
X5J  N28  C15  SING  N  N   9  
X5J  N28  C6   SING  N  N  10  
X5J  C1   C6   SING  Y  N  11  
X5J  C1   C2   DOUB  Y  N  12  
X5J  C15  C11  SING  N  N  13  
X5J  C6   N22  DOUB  Y  N  14  
X5J  O36  C18  SING  N  N  15  
X5J  C14  C16  SING  N  N  16  
X5J  C2   N21  SING  Y  N  17  
X5J  N27  C9   SING  N  N  18  
X5J  N22  C3   SING  Y  N  19  
X5J  N21  C3   DOUB  Y  N  20  
X5J  C9   N26  SING  N  N  21  
X5J  C9   N24  DOUB  N  N  22  
X5J  N26  C8   SING  N  N  23  
X5J  N24  C7   SING  N  N  24  
X5J  C16  C11  SING  N  N  25  
X5J  C16  O35  SING  N  N  26  
X5J  C18  C19  SING  N  N  27  
X5J  C18  C20  SING  N  N  28  
X5J  O37  C19  SING  N  N  29  
X5J  C8   O29  DOUB  N  N  30  
X5J  C8   C5   SING  N  N  31  
X5J  C7   C5   DOUB  Y  N  32  
X5J  C7   N25  SING  Y  N  33  
X5J  C19  C17  SING  N  N  34  
X5J  C5   N23  SING  Y  N  35  
X5J  C20  N25  SING  N  N  36  
X5J  C20  O34  SING  N  N  37  
X5J  N25  C4   SING  Y  N  38  
X5J  O35  P39  SING  N  N  39  
X5J  N23  C4   DOUB  Y  N  40  
X5J  C17  O34  SING  N  N  41  
X5J  C17  C13  SING  N  N  42  
X5J  P39  O33  SING  N  N  43  
X5J  P39  O31  DOUB  N  N  44  
X5J  P39  S41  SING  N  N  45  
X5J  O33  C13  SING  N  N  46  
X5J  C4   H1   SING  N  N  47  
X5J  C10  H2   SING  N  N  48  
X5J  C10  H3   SING  N  N  49  
X5J  C13  H4   SING  N  N  50  
X5J  C13  H5   SING  N  N  51  
X5J  C15  H6   SING  N  N  52  
X5J  C17  H7   SING  N  N  53  
X5J  C20  H8   SING  N  N  54  
X5J  C1   H9   SING  N  N  55  
X5J  C2   H10  SING  N  N  56  
X5J  C3   H11  SING  N  N  57  
X5J  C11  H12  SING  N  N  58  
X5J  C11  H13  SING  N  N  59  
X5J  C12  H14  SING  N  N  60  
X5J  C12  H15  SING  N  N  61  
X5J  C14  H16  SING  N  N  62  
X5J  C16  H17  SING  N  N  63  
X5J  C18  H18  SING  N  N  64  
X5J  C19  H19  SING  N  N  65  
X5J  N26  H20  SING  N  N  66  
X5J  N27  H21  SING  N  N  67  
X5J  N27  H22  SING  N  N  68  
X5J  N28  H23  SING  N  N  69  
X5J  O37  H24  SING  N  N  70  
X5J  S40  H25  SING  N  N  71  
X5J  S41  H26  SING  N  N  72  
#   #
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
X5J  SMILES            ACDLabs               12.01  "c1nc6c(n1C2OC3COP(=O)(OC4CC(CC4COP(=O)(OC2C3O)S)Nc5ncncc5)S)N=C(NC6=O)N"  
X5J  InChI             InChI                 1.03   "InChI=1S/C20H26N8O9P2S2/c21-20-26-17-14(18(30)27-20)24-8-28(17)19-16-15(29)12(35-19)6-34-38(31,40)36-11-4-10(25-13-1-2-22-7-23-13)3-9(11)5-33-39(32,41)37-16/h1-2,7-12,15-16,19,29H,3-6H2,(H,31,40)(H,32,41)(H,22,23,25)(H3,21,26,27,30)/t9-,10-,11+,12-,15-,16-,19-,38-,39-/m1/s1"  
X5J  InChIKey          InChI                 1.03   DXJHOSYLPZBMEZ-FEFYGENMSA-N  
X5J  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)Nc6ccncn6"  
X5J  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)Nc6ccncn6"  
X5J  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1cncnc1N[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"  
X5J  SMILES            "OpenEye OEToolkits"  2.0.7  "c1cncnc1NC2CC3COP(=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
X5J  "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)amino]-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"  
X5J  "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-ylamino)-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
X5J  "Create component"  2020-11-30  RCSB  
X5J  "Initial release"   2021-06-02  RCSB  
##
