data_X5D
#

_chem_comp.id                                   X5D
_chem_comp.name                                 "(2R,5R,7R,8R,10S,12aR,14R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2,10,16-trihydroxy-14-[(pyrimidin-4-yl)oxy]decahydro-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 O12 P2"
_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                   2022-02-04
_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                       617.400
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    X5D
_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       7KVZ
_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
X5D  C4   C1   C  0  1  Y  N  N  41.027   7.908  19.421   2.181   0.399  -2.521  C4   X5D   1  
X5D  C5   C2   C  0  1  Y  N  N  39.747   9.447  18.737   2.042   2.517  -2.086  C5   X5D   2  
X5D  C6   C3   C  0  1  Y  N  N  46.020   9.234  17.006  -5.688   1.031   0.408  C6   X5D   3  
X5D  C7   C4   C  0  1  Y  N  N  39.117   8.282  18.388   2.784   1.931  -1.055  C7   X5D   4  
X5D  C8   C5   C  0  1  N  N  N  39.124  10.690  18.406   1.803   3.911  -2.040  C8   X5D   5  
X5D  C10  C6   C  0  1  N  N  N  45.868   5.762  15.840  -2.852  -0.394   2.150  C10  X5D   6  
X5D  C13  C7   C  0  1  N  N  N  41.862   4.068  20.722   2.119  -3.141  -1.871  C13  X5D   7  
X5D  C15  C8   C  0  1  N  N  S  44.960   5.648  18.041  -1.809  -1.217   0.063  C15  X5D   8  
X5D  C17  C9   C  0  1  N  N  R  40.780   5.172  17.875   2.596  -0.939   0.550  C17  X5D   9  
X5D  C20  C10  C  0  1  N  N  R  39.754   5.869  18.724   3.534  -0.432  -0.558  C20  X5D  10  
X5D  C1   C11  C  0  1  Y  N  N  45.293  10.352  16.693  -6.226   2.291   0.146  C1   X5D  11  
X5D  C2   C12  C  0  1  Y  N  N  45.854  11.532  17.129  -7.540   2.368  -0.275  C2   X5D  12  
X5D  C3   C13  C  0  1  Y  N  N  47.613  10.445  18.043  -7.702   0.077  -0.159  C3   X5D  13  
X5D  C9   C14  C  0  1  N  N  N  37.366   9.242  17.445   3.023   3.986  -0.028  C9   X5D  14  
X5D  C11  C15  C  0  1  N  N  N  46.302   6.328  18.091  -3.298  -0.986  -0.217  C11  X5D  15  
X5D  C12  C16  C  0  1  N  N  N  43.670   4.575  16.159  -0.394  -0.077   1.788  C12  X5D  16  
X5D  C14  C17  C  0  1  N  N  R  45.019   4.893  16.746  -1.580  -1.015   1.564  C14  X5D  17  
X5D  C16  C18  C  0  1  N  N  R  40.578   4.040  19.922   3.267  -2.751  -0.936  C16  X5D  18  
X5D  C18  C19  C  0  1  N  N  R  46.408   6.878  16.705  -3.927  -0.421   1.060  C18  X5D  19  
X5D  C19  C20  C  0  1  N  N  R  40.780   3.780  18.462   2.701  -2.480   0.473  C19  X5D  20  
X5D  N21  N1   N  0  1  Y  N  N  47.009  11.609  17.804  -8.240   1.252  -0.415  N21  X5D  21  
X5D  N22  N2   N  0  1  Y  N  N  47.176   9.240  17.674  -6.453  -0.042   0.245  N22  X5D  22  
X5D  N23  N3   N  0  1  Y  N  N  40.930   9.214  19.377   1.701   1.530  -2.949  N23  X5D  23  
X5D  N24  N4   N  0  1  N  N  N  37.937   8.119  17.747   3.250   2.691  -0.058  N24  X5D  24  
X5D  N25  N5   N  0  1  Y  N  N  39.955   7.298  18.836   2.855   0.596  -1.351  N25  X5D  25  
X5D  N26  N6   N  0  1  N  N  N  37.931  10.454  17.759   2.306   4.614  -1.002  N26  X5D  26  
X5D  N27  N7   N  0  1  N  N  N  36.170   9.345  16.794   3.522   4.726   1.015  N27  X5D  27  
X5D  O28  O1   O  0  1  N  N  N  39.607  11.787  18.678   1.160   4.464  -2.916  O28  X5D  28  
X5D  O29  O2   O  0  1  N  N  N  41.478   4.901  14.113   2.477  -0.594   4.292  O29  X5D  29  
X5D  O30  O3   O  0  1  N  N  N  44.794   4.142  21.589  -1.208  -4.055  -2.452  O30  X5D  30  
X5D  O31  O4   O  0  1  N  N  N  42.912   5.780  16.084   0.543  -0.692   2.673  O31  X5D  31  
X5D  O32  O5   O  0  1  N  N  N  42.643   5.230  20.513   0.932  -3.346  -1.099  O32  X5D  32  
X5D  O33  O6   O  0  1  N  N  N  39.858   5.271  20.006   3.872  -1.540  -1.393  O33  X5D  33  
X5D  O34  O7   O  0  1  N  N  N  44.834   4.721  19.100  -1.446  -2.548  -0.310  O34  X5D  34  
X5D  O35  O8   O  0  1  N  N  N  40.426   5.145  16.499   3.023  -0.476   1.830  O35  X5D  35  
X5D  O36  O9   O  0  1  N  N  N  39.651   3.058  17.965   3.596  -2.970   1.474  O36  X5D  36  
X5D  O37  O10  O  0  1  N  N  N  40.952   7.251  15.201   1.878   1.536   3.078  O37  X5D  37  
X5D  O38  O11  O  0  1  N  N  N  44.726   6.700  20.723  -0.399  -1.664  -2.430  O38  X5D  38  
X5D  O39  O12  O  0  1  N  N  N  45.541   8.016  16.603  -4.403   0.904   0.818  O39  X5D  39  
X5D  P40  P1   P  0  1  N  N  N  41.447   5.724  15.380   1.990  -0.068   2.997  P40  X5D  40  
X5D  P41  P2   P  0  1  N  N  N  44.277   5.142  20.566  -0.527  -2.877  -1.591  P41  X5D  41  
X5D  H1   H1   H  0  1  N  N  N  41.856   7.378  19.867   2.059  -0.554  -3.014  H1   X5D  42  
X5D  H2   H2   H  0  1  N  N  N  45.255   6.175  15.025  -3.184  -0.975   3.011  H2   X5D  43  
X5D  H3   H3   H  0  1  N  N  N  46.696   5.175  15.416  -2.657   0.635   2.451  H3   X5D  44  
X5D  H4   H4   H  0  1  N  N  N  41.606   4.010  21.790   1.950  -2.343  -2.593  H4   X5D  45  
X5D  H5   H5   H  0  1  N  N  N  42.464   3.191  20.442   2.373  -4.061  -2.398  H5   X5D  46  
X5D  H6   H6   H  0  1  N  N  N  44.145   6.386  18.031  -1.214  -0.501  -0.502  H6   X5D  47  
X5D  H7   H7   H  0  1  N  N  N  41.766   5.638  18.021   1.573  -0.625   0.353  H7   X5D  48  
X5D  H8   H8   H  0  1  N  N  N  38.757   5.673  18.302   4.439  -0.016  -0.114  H8   X5D  49  
X5D  H9   H9   H  0  1  N  N  N  44.360  10.312  16.151  -5.631   3.183   0.269  H9   X5D  50  
X5D  H10  H10  H  0  1  N  N  N  45.331  12.452  16.914  -7.990   3.326  -0.488  H10  X5D  51  
X5D  H11  H11  H  0  1  N  N  N  48.545  10.481  18.587  -8.301  -0.813  -0.282  H11  X5D  52  
X5D  H12  H12  H  0  1  N  N  N  47.109   5.610  18.302  -3.414  -0.273  -1.033  H12  X5D  53  
X5D  H13  H13  H  0  1  N  N  N  46.319   7.130  18.844  -3.776  -1.930  -0.480  H13  X5D  54  
X5D  H14  H14  H  0  1  N  N  N  43.149   3.848  16.800   0.090   0.130   0.833  H14  X5D  55  
X5D  H15  H15  H  0  1  N  N  N  43.795   4.152  15.151  -0.747   0.857   2.225  H15  X5D  56  
X5D  H16  H16  H  0  1  N  N  N  45.554   3.948  16.918  -1.389  -1.976   2.040  H16  X5D  57  
X5D  H17  H17  H  0  1  N  N  N  39.949   3.233  20.326   4.003  -3.551  -0.893  H17  X5D  58  
X5D  H18  H18  H  0  1  N  N  N  47.449   7.117  16.444  -4.755  -1.057   1.375  H18  X5D  59  
X5D  H19  H19  H  0  1  N  N  N  41.732   3.263  18.270   1.717  -2.935   0.583  H19  X5D  60  
X5D  H20  H20  H  0  1  N  N  N  37.413  11.264  17.484   2.157   5.571  -0.950  H20  X5D  61  
X5D  H21  H21  H  0  1  N  N  N  35.678   8.519  16.519   4.033   4.292   1.716  H21  X5D  62  
X5D  H22  H22  H  0  1  N  N  N  35.786  10.246  16.592   3.363   5.682   1.051  H22  X5D  63  
X5D  H23  H23  H  0  1  N  N  N  45.344   4.590  22.221  -0.707  -4.305  -3.240  H23  X5D  64  
X5D  H24  H24  H  0  1  N  N  N  39.648   2.182  18.332   3.700  -3.931   1.472  H24  X5D  65  
X5D  H25  H25  H  0  1  N  N  N  40.745   7.412  14.288   1.271   1.854   3.761  H25  X5D  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
X5D  O29  P40  DOUB  N  N   1  
X5D  O37  P40  SING  N  N   2  
X5D  P40  O31  SING  N  N   3  
X5D  P40  O35  SING  N  N   4  
X5D  C10  C18  SING  N  N   5  
X5D  C10  C14  SING  N  N   6  
X5D  O31  C12  SING  N  N   7  
X5D  C12  C14  SING  N  N   8  
X5D  O35  C17  SING  N  N   9  
X5D  O39  C18  SING  N  N  10  
X5D  O39  C6   SING  N  N  11  
X5D  C1   C6   SING  Y  N  12  
X5D  C1   C2   DOUB  Y  N  13  
X5D  C18  C11  SING  N  N  14  
X5D  C14  C15  SING  N  N  15  
X5D  N27  C9   SING  N  N  16  
X5D  C6   N22  DOUB  Y  N  17  
X5D  C2   N21  SING  Y  N  18  
X5D  C9   N24  DOUB  N  N  19  
X5D  C9   N26  SING  N  N  20  
X5D  N22  C3   SING  Y  N  21  
X5D  N24  C7   SING  N  N  22  
X5D  N26  C8   SING  N  N  23  
X5D  N21  C3   DOUB  Y  N  24  
X5D  C17  C19  SING  N  N  25  
X5D  C17  C20  SING  N  N  26  
X5D  O36  C19  SING  N  N  27  
X5D  C15  C11  SING  N  N  28  
X5D  C15  O34  SING  N  N  29  
X5D  C7   C5   DOUB  Y  N  30  
X5D  C7   N25  SING  Y  N  31  
X5D  C8   O28  DOUB  N  N  32  
X5D  C8   C5   SING  N  N  33  
X5D  C19  C16  SING  N  N  34  
X5D  C20  N25  SING  N  N  35  
X5D  C20  O33  SING  N  N  36  
X5D  C5   N23  SING  Y  N  37  
X5D  N25  C4   SING  Y  N  38  
X5D  O34  P41  SING  N  N  39  
X5D  N23  C4   DOUB  Y  N  40  
X5D  C16  O33  SING  N  N  41  
X5D  C16  C13  SING  N  N  42  
X5D  O32  P41  SING  N  N  43  
X5D  O32  C13  SING  N  N  44  
X5D  P41  O38  DOUB  N  N  45  
X5D  P41  O30  SING  N  N  46  
X5D  C4   H1   SING  N  N  47  
X5D  C10  H2   SING  N  N  48  
X5D  C10  H3   SING  N  N  49  
X5D  C13  H4   SING  N  N  50  
X5D  C13  H5   SING  N  N  51  
X5D  C15  H6   SING  N  N  52  
X5D  C17  H7   SING  N  N  53  
X5D  C20  H8   SING  N  N  54  
X5D  C1   H9   SING  N  N  55  
X5D  C2   H10  SING  N  N  56  
X5D  C3   H11  SING  N  N  57  
X5D  C11  H12  SING  N  N  58  
X5D  C11  H13  SING  N  N  59  
X5D  C12  H14  SING  N  N  60  
X5D  C12  H15  SING  N  N  61  
X5D  C14  H16  SING  N  N  62  
X5D  C16  H17  SING  N  N  63  
X5D  C18  H18  SING  N  N  64  
X5D  C19  H19  SING  N  N  65  
X5D  N26  H20  SING  N  N  66  
X5D  N27  H21  SING  N  N  67  
X5D  N27  H22  SING  N  N  68  
X5D  O30  H23  SING  N  N  69  
X5D  O36  H24  SING  N  N  70  
X5D  O37  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
X5D  SMILES            ACDLabs               12.01  "c1nc6c(n1C5C3C(C(COP(O)(OC2CC(CC2COP(=O)(O3)O)Oc4ncncc4)=O)O5)O)N=C(NC6=O)N"  
X5D  InChI             InChI                 1.03   "InChI=1S/C20H25N7O12P2/c21-20-25-17-14(18(29)26-20)24-8-27(17)19-16-15(28)12(37-19)6-35-40(30,31)38-11-4-10(36-13-1-2-22-7-23-13)3-9(11)5-34-41(32,33)39-16/h1-2,7-12,15-16,19,28H,3-6H2,(H,30,31)(H,32,33)(H3,21,25,26,29)/t9-,10-,11+,12-,15-,16-,19-/m1/s1"  
X5D  InChIKey          InChI                 1.03   IQDCEFNXFAZHCY-SECPXAEJSA-N  
X5D  SMILES_CANONICAL  CACTVS                3.385  "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@@H]4CO[P](O)(=O)O[C@H]5C[C@@H](C[C@@H]5CO[P](O)(=O)O[C@@H]3[C@@H]4O)Oc6ccncn6"  
X5D  SMILES            CACTVS                3.385  "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH]4CO[P](O)(=O)O[CH]5C[CH](C[CH]5CO[P](O)(=O)O[CH]3[CH]4O)Oc6ccncn6"  
X5D  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1cncnc1O[C@@H]2C[C@@H]3COP(=O)(O[C@@H]4[C@@H]([C@@H](COP(=O)(O[C@H]3C2)O)O[C@H]4n5cnc6c5N=C(NC6=O)N)O)O"  
X5D  SMILES            "OpenEye OEToolkits"  2.0.7  "c1cncnc1OC2CC3COP(=O)(OC4C(C(COP(=O)(OC3C2)O)OC4n5cnc6c5N=C(NC6=O)N)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
X5D  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2R,5R,7R,8R,10S,12aR,14R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2,10,16-trihydroxy-14-[(pyrimidin-4-yl)oxy]decahydro-2H,10H-5,8-methano-2lambda~5~,10lambda~5~-cyclopenta[l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecine-2,10-dione"  
X5D  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "2-azanyl-9-[(1~{R},6~{R},8~{R},10~{S},15~{R},17~{R},18~{R})-3,12,18-tris(oxidanyl)-3,12-bis(oxidanylidene)-8-pyrimidin-4-yloxy-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
X5D  "Create component"  2020-11-30  RCSB  
X5D  "Initial release"   2022-02-09  RCSB  
##
