data_8GD
#

_chem_comp.id                                   8GD
_chem_comp.name                                 "2'-deoxy-8-oxoguanosine 5'-(trihydrogen diphosphate)"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H15 N5 O11 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "8-oxo-7,8-dihydro-2'-deoxy-guanosine-5'-diphosphate"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2010-01-09
_chem_comp.pdbx_modified_date                   2021-03-13
_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                       443.201
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    8GD
_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       3AC9
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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
8GD  N1      N1      N  0  1  N  N  N  -18.192  22.624  78.146  -6.205   1.971   0.364  N1      8GD   1  
8GD  C2      C2      C  0  1  N  N  N  -18.256  21.427  77.469  -5.560   1.533   1.480  C2      8GD   2  
8GD  N2      N2      N  0  1  N  N  N  -17.109  20.959  76.949  -6.022   1.918   2.713  N2      8GD   3  
8GD  N3      N3      N  0  1  N  N  N  -19.374  20.733  77.315  -4.505   0.751   1.407  N3      8GD   4  
8GD  C4      C4      C  0  1  N  N  N  -20.436  21.347  77.898  -4.022   0.352   0.225  C4      8GD   5  
8GD  C5      C5      C  0  1  N  N  N  -20.472  22.536  78.585  -4.642   0.770  -0.946  C5      8GD   6  
8GD  C6      C6      C  0  1  N  N  N  -19.276  23.265  78.745  -5.766   1.604  -0.861  C6      8GD   7  
8GD  O6      O6      O  0  1  N  N  N  -19.116  24.342  79.328  -6.336   1.988  -1.869  O6      8GD   8  
8GD  N7      N7      N  0  1  N  N  N  -21.758  22.811  79.018  -3.930   0.206  -2.008  N7      8GD   9  
8GD  C8      C8      C  0  1  N  N  N  -22.482  21.805  78.598  -2.921  -0.522  -1.489  C8      8GD  10  
8GD  O8      O8      O  0  1  N  N  N  -23.692  21.742  78.822  -2.103  -1.150  -2.135  O8      8GD  11  
8GD  N9      N9      N  0  1  N  N  N  -21.728  20.879  77.907  -2.959  -0.447  -0.146  N9      8GD  12  
8GD  PA      PA      P  0  1  N  N  N  -23.546  19.018  71.774   3.743  -0.566  -0.203  PA      8GD  13  
8GD  PB      PB      P  0  1  N  N  N  -25.834  17.918  73.282   5.523   1.778   0.146  PB      8GD  14  
8GD  "C1'"   "C1'"   C  0  1  N  N  R  -22.131  19.617  77.260  -2.026  -1.105   0.772  "C1'"   8GD  15  
8GD  O1A     O1A     O  0  1  N  N  N  -23.452  18.326  70.463   3.621  -0.304  -1.655  O1A     8GD  16  
8GD  O1B     O1B     O  0  1  N  N  N  -26.638  18.043  72.058   6.962   1.085   0.352  O1B     8GD  17  
8GD  "C2'"   "C2'"   C  0  1  N  N  N  -23.557  19.621  76.739  -2.172  -2.635   0.660  "C2'"   8GD  18  
8GD  O2A     O2A     O  0  1  N  N  N  -24.145  20.390  71.822   4.710  -1.831   0.034  O2A     8GD  19  
8GD  O2B     O2B     O  0  1  N  N  N  -26.090  18.797  74.400   5.372   2.190  -1.267  O2B     8GD  20  
8GD  "C3'"   "C3'"   C  0  1  N  N  S  -23.459  18.647  75.571  -0.759  -3.122   0.256  "C3'"   8GD  21  
8GD  "O3'"   "O3'"   O  0  1  N  N  N  -23.516  17.312  76.064  -0.412  -4.318   0.958  "O3'"   8GD  22  
8GD  O3A     O3A     O  0  1  N  N  N  -24.319  18.009  72.807   4.363   0.728   0.526  O3A     8GD  23  
8GD  O3B     O3B     O  0  1  N  N  N  -25.973  16.426  73.804   5.409   3.071   1.098  O3B     8GD  24  
8GD  "C4'"   "C4'"   C  0  1  N  N  R  -22.058  18.895  75.008   0.134  -1.938   0.705  "C4'"   8GD  25  
8GD  "O4'"   "O4'"   O  0  1  N  N  N  -21.293  19.439  76.117  -0.673  -0.777   0.412  "O4'"   8GD  26  
8GD  "C5'"   "C5'"   C  0  1  N  N  N  -21.990  19.788  73.770   1.434  -1.908  -0.102  "C5'"   8GD  27  
8GD  "O5'"   "O5'"   O  0  1  N  N  N  -22.167  18.981  72.578   2.287  -0.881   0.409  "O5'"   8GD  28  
8GD  HN1     HN1     H  0  1  N  N  N  -17.299  23.068  78.213  -6.983   2.544   0.448  HN1     8GD  29  
8GD  HN2     HN2     H  0  1  N  N  N  -17.103  20.092  76.450  -6.799   2.495   2.782  HN2     8GD  30  
8GD  HN2A    HN2A    H  0  0  N  N  N  -16.261  21.477  77.061  -5.571   1.614   3.517  HN2A    8GD  31  
8GD  HN7     HN7     H  0  1  N  N  N  -22.067  23.607  79.539  -4.127   0.318  -2.951  HN7     8GD  32  
8GD  "H1'"   "H1'"   H  0  1  N  N  N  -22.046  18.826  78.019  -2.226  -0.787   1.795  "H1'"   8GD  33  
8GD  HO1B    HO1B    H  0  0  N  N  N  -27.274  18.741  72.166   7.130   0.789   1.257  HO1B    8GD  34  
8GD  "H2'"   "H2'"   H  0  1  N  N  N  -24.278  19.287  77.499  -2.462  -3.061   1.620  "H2'"   8GD  35  
8GD  "H2'A"  "H2'A"  H  0  0  N  N  N  -23.879  20.623  76.419  -2.900  -2.893  -0.109  "H2'A"  8GD  36  
8GD  HO2A    HO2A    H  0  0  N  N  N  -24.403  20.654  70.947   4.836  -2.061   0.965  HO2A    8GD  37  
8GD  "H3'"   "H3'"   H  0  1  N  N  N  -24.263  18.782  74.833  -0.694  -3.273  -0.822  "H3'"   8GD  38  
8GD  "HO3'"  "HO3'"  H  0  0  N  N  N  -23.455  16.703  75.338  -1.000  -5.064   0.778  "HO3'"  8GD  39  
8GD  HO3B    HO3B    H  0  0  N  N  N  -26.192  16.433  74.728   6.079   3.747   0.925  HO3B    8GD  40  
8GD  "H4'"   "H4'"   H  0  1  N  N  N  -21.648  17.948  74.626   0.345  -1.999   1.772  "H4'"   8GD  41  
8GD  "H5'"   "H5'"   H  0  1  N  N  N  -22.786  20.545  73.821   1.935  -2.872  -0.019  "H5'"   8GD  42  
8GD  "H5'A"  "H5'A"  H  0  0  N  N  N  -21.010  20.287  73.732   1.207  -1.705  -1.148  "H5'A"  8GD  43  
#   #
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
8GD  N1     C2      SING  N  N   1  
8GD  N1     C6      SING  N  N   2  
8GD  C2     N2      SING  N  N   3  
8GD  C2     N3      DOUB  N  N   4  
8GD  N3     C4      SING  N  N   5  
8GD  C4     C5      DOUB  N  N   6  
8GD  C4     N9      SING  N  N   7  
8GD  C5     C6      SING  N  N   8  
8GD  C5     N7      SING  N  N   9  
8GD  C6     O6      DOUB  N  N  10  
8GD  N7     C8      SING  N  N  11  
8GD  C8     O8      DOUB  N  N  12  
8GD  C8     N9      SING  N  N  13  
8GD  N9     "C1'"   SING  N  N  14  
8GD  PA     O1A     DOUB  N  N  15  
8GD  PA     O2A     SING  N  N  16  
8GD  PA     O3A     SING  N  N  17  
8GD  PA     "O5'"   SING  N  N  18  
8GD  PB     O1B     SING  N  N  19  
8GD  PB     O2B     DOUB  N  N  20  
8GD  PB     O3A     SING  N  N  21  
8GD  PB     O3B     SING  N  N  22  
8GD  "C1'"  "C2'"   SING  N  N  23  
8GD  "C1'"  "O4'"   SING  N  N  24  
8GD  "C2'"  "C3'"   SING  N  N  25  
8GD  "C3'"  "O3'"   SING  N  N  26  
8GD  "C3'"  "C4'"   SING  N  N  27  
8GD  "C4'"  "O4'"   SING  N  N  28  
8GD  "C4'"  "C5'"   SING  N  N  29  
8GD  "C5'"  "O5'"   SING  N  N  30  
8GD  N1     HN1     SING  N  N  31  
8GD  N2     HN2     SING  N  N  32  
8GD  N2     HN2A    SING  N  N  33  
8GD  N7     HN7     SING  N  N  34  
8GD  "C1'"  "H1'"   SING  N  N  35  
8GD  O1B    HO1B    SING  N  N  36  
8GD  "C2'"  "H2'"   SING  N  N  37  
8GD  "C2'"  "H2'A"  SING  N  N  38  
8GD  O2A    HO2A    SING  N  N  39  
8GD  "C3'"  "H3'"   SING  N  N  40  
8GD  "O3'"  "HO3'"  SING  N  N  41  
8GD  O3B    HO3B    SING  N  N  42  
8GD  "C4'"  "H4'"   SING  N  N  43  
8GD  "C5'"  "H5'"   SING  N  N  44  
8GD  "C5'"  "H5'A"  SING  N  N  45  
#   #
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
8GD  SMILES_CANONICAL  CACTVS                3.352  "NC1=NC2=C(NC(=O)N2[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(O)=O)O3)C(=O)N1"  
8GD  SMILES            CACTVS                3.352  "NC1=NC2=C(NC(=O)N2[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O3)C(=O)N1"  
8GD  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.0  "C1[C@@H]([C@H](O[C@H]1N2C3=C(C(=O)NC(=N3)N)NC2=O)CO[P@](=O)(O)OP(=O)(O)O)O"  
8GD  SMILES            "OpenEye OEToolkits"  1.7.0  "C1C(C(OC1N2C3=C(C(=O)NC(=N3)N)NC2=O)COP(=O)(O)OP(=O)(O)O)O"  
8GD  InChI             InChI                 1.03   "InChI=1S/C10H15N5O11P2/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(25-5)2-24-28(22,23)26-27(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1"  
8GD  InChIKey          InChI                 1.03   LJMLTZSNWOCYNQ-VPENINKCSA-N  
#
_pdbx_chem_comp_identifier.comp_id          8GD
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  1.6.1
_pdbx_chem_comp_identifier.identifier       "[(2R,3S,5R)-5-(2-azanyl-6,8-dioxo-1,7-dihydropurin-9-yl)-3-hydroxy-oxolan-2-yl]methyl phosphono hydrogen 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
8GD  "Create component"   2010-01-09  PDBJ  
8GD  "Modify descriptor"  2011-06-04  RCSB  
8GD  "Modify synonyms"    2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     8GD
_pdbx_chem_comp_synonyms.name        "8-oxo-7,8-dihydro-2'-deoxy-guanosine-5'-diphosphate"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
