data_8PY
#

_chem_comp.id                                   8PY
_chem_comp.name                                 "[(2~{R},3~{S},5~{R})-5-[2-azanyl-8-[ethanoyl(pyren-2-yl)amino]-6-oxidanylidene-1~{H}-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C28 H25 N6 O8 P"
_chem_comp.mon_nstd_parent_comp_id              DG
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2016-04-22
_chem_comp.pdbx_modified_date                   2019-05-07
_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                       604.507
_chem_comp.one_letter_code                      G
_chem_comp.three_letter_code                    8PY
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  Y
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       5g35
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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
8PY  P      P1   P  0  1  N  N  N  24.144  59.534  -22.951   6.899  -1.826   0.380  P      8PY   1  
8PY  OP1    O1   O  0  1  N  N  N  24.063  60.090  -21.536   7.430  -0.613  -0.281  OP1    8PY   2  
8PY  "O5'"  O2   O  0  1  N  N  N  22.842  59.903  -23.821   5.290  -1.814   0.312  "O5'"  8PY   3  
8PY  "C5'"  C1   C  0  1  N  N  N  21.772  58.978  -23.779   4.564  -1.689  -0.913  "C5'"  8PY   4  
8PY  "C4'"  C2   C  0  1  N  N  R  21.275  58.713  -25.198   3.063  -1.713  -0.620  "C4'"  8PY   5  
8PY  "C3'"  C3   C  0  1  N  N  S  20.635  57.346  -25.260   2.257  -1.666  -1.937  "C3'"  8PY   6  
8PY  "O3'"  O3   O  0  1  N  N  N  19.239  57.373  -24.894   1.837  -2.979  -2.314  "O3'"  8PY   7  
8PY  "C2'"  C4   C  0  1  N  N  N  20.869  56.902  -26.684   1.035  -0.783  -1.599  "C2'"  8PY   8  
8PY  "C1'"  C5   C  0  1  N  N  R  21.723  57.985  -27.323   1.247  -0.401  -0.117  "C1'"  8PY   9  
8PY  "O4'"  O4   O  0  1  N  N  N  22.285  58.656  -26.184   2.671  -0.522   0.097  "O4'"  8PY  10  
8PY  N9     N1   N  0  1  Y  N  N  22.611  57.200  -28.225   0.810   0.977   0.122  N9     8PY  11  
8PY  C4     C6   C  0  1  Y  N  N  23.217  56.083  -27.834   1.360   2.108  -0.424  C4     8PY  12  
8PY  C5     C7   C  0  1  Y  N  N  23.938  55.561  -29.013   0.625   3.184   0.083  C5     8PY  13  
8PY  N7     N2   N  0  1  Y  N  N  23.710  56.374  -30.056  -0.328   2.673   0.904  N7     8PY  14  
8PY  C8     C8   C  0  1  Y  N  N  22.897  57.286  -29.523  -0.226   1.370   0.925  C8     8PY  15  
8PY  N3     N3   N  0  1  N  N  N  23.298  55.438  -26.655   2.373   2.337  -1.268  N3     8PY  16  
8PY  C2     C9   C  0  1  N  N  N  24.063  54.347  -26.629   2.692   3.559  -1.632  C2     8PY  17  
8PY  N2     N4   N  0  1  N  N  N  24.132  53.702  -25.481   3.739   3.744  -2.501  N2     8PY  18  
8PY  N1     N5   N  0  1  N  N  N  24.742  53.813  -27.659   2.012   4.647  -1.172  N1     8PY  19  
8PY  C6     C10  C  0  1  N  N  N  24.743  54.344  -28.873   0.977   4.494  -0.317  C6     8PY  20  
8PY  O6     O5   O  0  1  N  N  N  25.389  53.887  -29.853   0.363   5.461   0.101  O6     8PY  21  
8PY  OP2    O6   O  0  1  N  Y  N  24.451  58.042  -22.950   7.458  -3.135  -0.371  OP2    8PY  22  
8PY  N8     N6   N  0  1  N  N  N  22.559  58.255  -30.379  -1.037   0.516   1.658  N8     8PY  23  
8PY  C7     C11  C  0  1  N  N  N  23.145  59.469  -30.408  -0.621   0.050   2.852  C7     8PY  24  
8PY  C9     C12  C  0  1  N  N  N  22.480  60.522  -31.250   0.645   0.586   3.470  C9     8PY  25  
8PY  O10    O7   O  0  1  N  N  N  24.178  59.720  -29.798  -1.265  -0.800   3.430  O10    8PY  26  
8PY  C11    C13  C  0  1  Y  N  N  21.698  57.984  -31.364  -2.248   0.149   1.173  C11    8PY  27  
8PY  C12    C14  C  0  1  Y  N  N  22.392  57.858  -32.525  -3.258   1.106   1.111  C12    8PY  28  
8PY  C13    C15  C  0  1  Y  N  N  21.735  57.627  -33.673  -4.517   0.777   0.615  C13    8PY  29  
8PY  C14    C16  C  0  1  Y  N  N  20.365  57.539  -33.555  -4.751  -0.605   0.158  C14    8PY  30  
8PY  C15    C17  C  0  1  Y  N  N  19.640  57.668  -32.359  -3.653  -1.586   0.241  C15    8PY  31  
8PY  C16    C18  C  0  1  Y  N  N  20.325  57.910  -31.202  -2.428  -1.165   0.752  C16    8PY  32  
8PY  C23    C19  C  0  1  Y  N  N  19.674  57.276  -34.794  -5.916  -0.957  -0.314  C23    8PY  33  
8PY  C24    C20  C  0  1  Y  N  N  18.233  57.163  -34.747  -6.150  -2.339  -0.770  C24    8PY  34  
8PY  C25    C21  C  0  1  Y  N  N  17.586  57.308  -33.524  -5.117  -3.269  -0.694  C25    8PY  35  
8PY  C26    C22  C  0  1  Y  N  N  18.275  57.564  -32.335  -3.868  -2.892  -0.190  C26    8PY  36  
8PY  C27    C23  C  0  1  Y  N  N  20.426  57.117  -36.035  -7.014   0.024  -0.396  C27    8PY  37  
8PY  C28    C24  C  0  1  Y  N  N  21.817  57.237  -36.048  -6.799   1.331   0.033  C28    8PY  38  
8PY  C29    C25  C  0  1  Y  N  N  22.473  57.489  -34.862  -5.550   1.707   0.539  C29    8PY  39  
8PY  C30    C26  C  0  1  Y  N  N  17.588  56.915  -35.946  -7.411  -2.668  -1.264  C30    8PY  40  
8PY  C31    C27  C  0  1  Y  N  N  18.294  56.773  -37.122  -8.421  -1.712  -1.325  C31    8PY  41  
8PY  C32    C28  C  0  1  Y  N  N  19.693  56.874  -37.182  -8.241  -0.397  -0.905  C32    8PY  42  
8PY  H2     H2   H  0  1  N  N  N  20.952  59.393  -23.174   4.825  -0.747  -1.395  H2     8PY  43  
8PY  H3     H3   H  0  1  N  N  N  22.119  58.036  -23.330   4.819  -2.518  -1.572  H3     8PY  44  
8PY  H4     H4   H  0  1  N  N  N  20.525  59.473  -25.460   2.803  -2.604  -0.047  H4     8PY  45  
8PY  H5     H5   H  0  1  N  N  N  21.181  56.670  -24.585   2.850  -1.213  -2.731  H5     8PY  46  
8PY  H6     H6   H  0  1  N  N  N  19.153  57.658  -23.992   1.327  -3.008  -3.135  H6     8PY  47  
8PY  H7     H7   H  0  1  N  N  N  19.912  56.805  -27.217   1.023   0.109  -2.225  H7     8PY  48  
8PY  H8     H8   H  0  1  N  N  N  21.398  55.937  -26.702   0.111  -1.347  -1.722  H8     8PY  49  
8PY  H9     H9   H  0  1  N  N  N  21.088  58.665  -27.910   0.707  -1.089   0.533  H9     8PY  50  
8PY  H10    H10  H  0  1  N  N  N  23.625  54.038  -24.687   4.232   2.980  -2.837  H10    8PY  51  
8PY  H11    H11  H  0  1  N  N  N  24.691  52.877  -25.404   3.986   4.641  -2.778  H11    8PY  52  
8PY  H12    H12  H  0  1  N  N  N  25.270  52.978  -27.502   2.273   5.536  -1.460  H12    8PY  53  
8PY  H13    H13  H  0  1  N  N  N  24.535  57.736  -22.055   7.150  -3.969   0.009  H13    8PY  54  
8PY  H14    H14  H  0  1  N  N  N  23.062  61.454  -31.199   0.424   1.507   4.010  H14    8PY  55  
8PY  H15    H15  H  0  1  N  N  N  22.429  60.178  -32.294   1.051  -0.152   4.162  H15    8PY  56  
8PY  H16    H16  H  0  1  N  N  N  21.463  60.704  -30.874   1.374   0.789   2.686  H16    8PY  57  
8PY  H17    H17  H  0  1  N  N  N  23.469  57.943  -32.525  -3.063   2.112   1.451  H17    8PY  58  
8PY  H18    H18  H  0  1  N  N  N  19.839  58.033  -30.246  -1.607  -1.865   0.818  H18    8PY  59  
8PY  H19    H19  H  0  1  N  N  N  16.510  57.219  -33.492  -5.281  -4.284  -1.026  H19    8PY  60  
8PY  H20    H20  H  0  1  N  N  N  17.736  57.679  -31.406  -3.069  -3.616  -0.134  H20    8PY  61  
8PY  H21    H21  H  0  1  N  N  N  22.369  57.134  -36.971  -7.598   2.055  -0.024  H21    8PY  62  
8PY  H22    H22  H  0  1  N  N  N  23.549  57.580  -34.846  -5.387   2.722   0.872  H22    8PY  63  
8PY  H23    H23  H  0  1  N  N  N  16.511  56.831  -35.961  -7.606  -3.674  -1.604  H23    8PY  64  
8PY  H24    H24  H  0  1  N  N  N  17.749  56.576  -38.033  -9.385  -2.003  -1.714  H24    8PY  65  
8PY  H25    H25  H  0  1  N  N  N  20.199  56.761  -38.129  -9.060   0.303  -0.975  H25    8PY  66  
8PY  O1     O8   O  0  1  N  Y  N       ?       ?        ?   7.371  -1.849   1.920  O1     8PY  67  
8PY  H1     H1   H  0  1  N  N  N       ?       ?        ?   8.330  -1.857   2.037  H1     8PY  68  
#   #
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
8PY  C32    C31    DOUB  Y  N   1  
8PY  C32    C27    SING  Y  N   2  
8PY  C31    C30    SING  Y  N   3  
8PY  C28    C27    DOUB  Y  N   4  
8PY  C28    C29    SING  Y  N   5  
8PY  C27    C23    SING  Y  N   6  
8PY  C30    C24    DOUB  Y  N   7  
8PY  C29    C13    DOUB  Y  N   8  
8PY  C23    C24    SING  Y  N   9  
8PY  C23    C14    DOUB  Y  N  10  
8PY  C24    C25    SING  Y  N  11  
8PY  C13    C14    SING  Y  N  12  
8PY  C13    C12    SING  Y  N  13  
8PY  C14    C15    SING  Y  N  14  
8PY  C25    C26    DOUB  Y  N  15  
8PY  C12    C11    DOUB  Y  N  16  
8PY  C15    C26    SING  Y  N  17  
8PY  C15    C16    DOUB  Y  N  18  
8PY  C11    C16    SING  Y  N  19  
8PY  C11    N8     SING  N  N  20  
8PY  C9     C7     SING  N  N  21  
8PY  C7     N8     SING  N  N  22  
8PY  C7     O10    DOUB  N  N  23  
8PY  N8     C8     SING  N  N  24  
8PY  N7     C8     DOUB  Y  N  25  
8PY  N7     C5     SING  Y  N  26  
8PY  O6     C6     DOUB  N  N  27  
8PY  C8     N9     SING  Y  N  28  
8PY  C5     C6     SING  N  N  29  
8PY  C5     C4     DOUB  Y  N  30  
8PY  C6     N1     SING  N  N  31  
8PY  N9     C4     SING  Y  N  32  
8PY  N9     "C1'"  SING  N  N  33  
8PY  C4     N3     SING  N  N  34  
8PY  N1     C2     SING  N  N  35  
8PY  "C1'"  "C2'"  SING  N  N  36  
8PY  "C1'"  "O4'"  SING  N  N  37  
8PY  "C2'"  "C3'"  SING  N  N  38  
8PY  N3     C2     DOUB  N  N  39  
8PY  C2     N2     SING  N  N  40  
8PY  "O4'"  "C4'"  SING  N  N  41  
8PY  "C3'"  "C4'"  SING  N  N  42  
8PY  "C3'"  "O3'"  SING  N  N  43  
8PY  "C4'"  "C5'"  SING  N  N  44  
8PY  "O5'"  "C5'"  SING  N  N  45  
8PY  "O5'"  P      SING  N  N  46  
8PY  P      OP2    SING  N  N  47  
8PY  P      OP1    DOUB  N  N  48  
8PY  "C5'"  H2     SING  N  N  49  
8PY  "C5'"  H3     SING  N  N  50  
8PY  "C4'"  H4     SING  N  N  51  
8PY  "C3'"  H5     SING  N  N  52  
8PY  "O3'"  H6     SING  N  N  53  
8PY  "C2'"  H7     SING  N  N  54  
8PY  "C2'"  H8     SING  N  N  55  
8PY  "C1'"  H9     SING  N  N  56  
8PY  N2     H10    SING  N  N  57  
8PY  N2     H11    SING  N  N  58  
8PY  N1     H12    SING  N  N  59  
8PY  OP2    H13    SING  N  N  60  
8PY  C9     H14    SING  N  N  61  
8PY  C9     H15    SING  N  N  62  
8PY  C9     H16    SING  N  N  63  
8PY  C12    H17    SING  N  N  64  
8PY  C16    H18    SING  N  N  65  
8PY  C25    H19    SING  N  N  66  
8PY  C26    H20    SING  N  N  67  
8PY  C28    H21    SING  N  N  68  
8PY  C29    H22    SING  N  N  69  
8PY  C30    H23    SING  N  N  70  
8PY  C31    H24    SING  N  N  71  
8PY  C32    H25    SING  N  N  72  
8PY  P      O1     SING  N  N  73  
8PY  O1     H1     SING  N  N  74  
#   #
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
8PY  InChI             InChI                 1.03   "InChI=1S/C28H25N6O8P/c1-13(35)33(18-9-16-7-5-14-3-2-4-15-6-8-17(10-18)23(16)22(14)15)28-30-24-25(31-27(29)32-26(24)37)34(28)21-11-19(36)20(42-21)12-41-43(38,39)40/h2-10,19-21,36H,11-12H2,1H3,(H2,38,39,40)(H3,29,31,32,37)/t19-,20+,21+/m0/s1"  
8PY  InChIKey          InChI                 1.03   SOPYCICHZOSXGU-PWRODBHTSA-N  
8PY  SMILES_CANONICAL  CACTVS                3.385  "CC(=O)N(c1cc2ccc3cccc4ccc(c1)c2c34)c5nc6C(=O)NC(=Nc6n5[C@H]7C[C@H](O)[C@@H](CO[P](O)(O)=O)O7)N"  
8PY  SMILES            CACTVS                3.385  "CC(=O)N(c1cc2ccc3cccc4ccc(c1)c2c34)c5nc6C(=O)NC(=Nc6n5[CH]7C[CH](O)[CH](CO[P](O)(O)=O)O7)N"  
8PY  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.5  "CC(=O)N(c1cc2ccc3cccc4c3c2c(c1)cc4)c5nc6c(n5[C@H]7C[C@@H]([C@H](O7)COP(=O)(O)O)O)N=C(NC6=O)N"  
8PY  SMILES            "OpenEye OEToolkits"  2.0.5  "CC(=O)N(c1cc2ccc3cccc4c3c2c(c1)cc4)c5nc6c(n5C7CC(C(O7)COP(=O)(O)O)O)N=C(NC6=O)N"  
#
_pdbx_chem_comp_identifier.comp_id          8PY
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.5
_pdbx_chem_comp_identifier.identifier       "[(2~{R},3~{S},5~{R})-5-[2-azanyl-8-[ethanoyl(pyren-2-yl)amino]-6-oxidanylidene-1~{H}-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
8PY  "Create component"        2016-04-22  EBI   
8PY  "Initial release"         2016-06-01  RCSB  
8PY  "Other modification"      2016-06-02  RCSB  
8PY  "Modify one letter code"  2019-05-07  EBI   
##
