data_GDP
#

_chem_comp.id                                   GDP
_chem_comp.name                                 "GUANOSINE-5'-DIPHOSPHATE"
_chem_comp.type                                 "RNA LINKING"
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H15 N5 O11 P2"
_chem_comp.mon_nstd_parent_comp_id              G
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    1999-07-08
_chem_comp.pdbx_modified_date                   2014-05-12
_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                      G
_chem_comp.three_letter_code                    GDP
_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       1EK0
_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
GDP  PB      PB      P  0  1  N  N  N  13.635  17.027  28.402  -5.743  -1.471   0.475  PB      GDP   1  
GDP  O1B     O1B     O  0  1  N  N  N  14.317  18.299  28.131  -6.829  -0.831  -0.300  O1B     GDP   2  
GDP  O2B     O2B     O  0  1  N  N  N  14.465  15.868  28.851  -6.293  -1.885   1.930  O2B     GDP   3  
GDP  O3B     O3B     O  0  1  N  N  N  12.657  17.014  29.609  -5.234  -2.787  -0.301  O3B     GDP   4  
GDP  O3A     O3A     O  0  1  N  N  N  13.031  16.438  26.904  -4.519  -0.438   0.638  O3A     GDP   5  
GDP  PA      PA      P  0  1  N  N  N  12.164  17.382  25.843  -3.821   0.633  -0.340  PA      GDP   6  
GDP  O1A     O1A     O  0  1  N  N  N  11.308  16.310  25.239  -3.718   0.063  -1.702  O1A     GDP   7  
GDP  O2A     O2A     O  0  1  N  N  N  11.654  18.737  26.082  -4.708   1.976  -0.386  O2A     GDP   8  
GDP  "O5'"   "O5'"   O  0  1  N  N  N  13.417  17.470  24.852  -2.348   0.981   0.208  "O5'"   GDP   9  
GDP  "C5'"   "C5'"   C  0  1  N  N  N  14.543  18.324  25.037  -1.434   1.823  -0.497  "C5'"   GDP  10  
GDP  "C4'"   "C4'"   C  0  1  N  N  R  15.043  18.710  23.648  -0.133   1.943   0.299  "C4'"   GDP  11  
GDP  "O4'"   "O4'"   O  0  1  N  N  N  15.183  17.536  22.793   0.533   0.670   0.344  "O4'"   GDP  12  
GDP  "C3'"   "C3'"   C  0  1  N  N  S  13.926  19.400  22.829   0.820   2.933  -0.399  "C3'"   GDP  13  
GDP  "O3'"   "O3'"   O  0  1  N  N  N  14.002  20.787  23.226   1.125   4.028   0.467  "O3'"   GDP  14  
GDP  "C2'"   "C2'"   C  0  1  N  N  R  14.511  19.303  21.406   2.091   2.098  -0.686  "C2'"   GDP  15  
GDP  "O2'"   "O2'"   O  0  1  N  N  N  15.627  20.165  21.220   3.271   2.861  -0.428  "O2'"   GDP  16  
GDP  "C1'"   "C1'"   C  0  1  N  N  R  15.015  17.874  21.438   1.952   0.935   0.329  "C1'"   GDP  17  
GDP  N9      N9      N  0  1  Y  N  N  13.968  16.928  20.922   2.691  -0.243  -0.132  N9      GDP  18  
GDP  C8      C8      C  0  1  Y  N  N  13.129  16.056  21.555   2.200  -1.252  -0.908  C8      GDP  19  
GDP  N7      N7      N  0  1  Y  N  N  12.358  15.405  20.737   3.131  -2.134  -1.125  N7      GDP  20  
GDP  C5      C5      C  0  1  Y  N  N  12.701  15.869  19.474   4.272  -1.746  -0.504  C5      GDP  21  
GDP  C6      C6      C  0  1  N  N  N  12.214  15.545  18.183   5.571  -2.295  -0.396  C6      GDP  22  
GDP  O6      O6      O  0  1  N  N  N  11.326  14.728  17.882   5.850  -3.350  -0.939  O6      GDP  23  
GDP  N1      N1      N  0  1  N  N  N  12.870  16.282  17.187   6.495  -1.620   0.324  N1      GDP  24  
GDP  C2      C2      C  0  1  N  N  N  13.858  17.205  17.402   6.171  -0.441   0.927  C2      GDP  25  
GDP  N2      N2      N  0  1  N  N  N  14.348  17.795  16.316   7.130   0.222   1.651  N2      GDP  26  
GDP  N3      N3      N  0  1  N  N  N  14.329  17.524  18.614   4.968   0.079   0.834  N3      GDP  27  
GDP  C4      C4      C  0  1  Y  N  N  13.701  16.819  19.565   4.003  -0.529   0.133  C4      GDP  28  
GDP  HOB2    HOB2    H  0  0  N  N  N  15.376  16.131  28.902  -7.033  -2.508   1.908  HOB2    GDP  29  
GDP  HOB3    HOB3    H  0  0  N  N  N  12.643  17.873  30.015  -4.521  -3.259   0.151  HOB3    GDP  30  
GDP  HOA2    HOA2    H  0  0  N  N  N  10.749  18.789  25.799  -4.818   2.404   0.474  HOA2    GDP  31  
GDP  "H5'"   "H5'1"  H  0  1  N  N  N  14.247  19.224  25.596  -1.222   1.390  -1.475  "H5'"   GDP  32  
GDP  "H5''"  "H5'2"  H  0  0  N  N  N  15.333  17.793  25.589  -1.874   2.811  -0.625  "H5''"  GDP  33  
GDP  "H4'"   "H4'"   H  0  1  N  N  N  15.955  19.324  23.692  -0.349   2.285   1.312  "H4'"   GDP  34  
GDP  "H3'"   "H3'"   H  0  1  N  N  N  12.939  18.927  22.938   0.380   3.294  -1.329  "H3'"   GDP  35  
GDP  "HO3'"  "HO3'"  H  0  0  N  Y  N  13.340  21.286  22.762   1.722   4.683   0.078  "HO3'"  GDP  36  
GDP  "H2'"   "H2'"   H  0  1  N  N  N  13.729  19.439  20.644   2.088   1.724  -1.710  "H2'"   GDP  37  
GDP  "HO2'"  "HO2'"  H  0  0  N  N  N  15.954  20.073  20.333   3.357   3.652  -0.979  "HO2'"  GDP  38  
GDP  "H1'"   "H1'"   H  0  1  N  N  N  15.948  17.778  20.863   2.295   1.244   1.316  "H1'"   GDP  39  
GDP  H8      H8      H  0  1  N  N  N  13.109  15.921  22.626   1.190  -1.310  -1.285  H8      GDP  40  
GDP  HN1     HN1     H  0  1  N  N  N  12.593  16.120  16.240   7.392  -1.977   0.412  HN1     GDP  41  
GDP  HN21    HN21    H  0  0  N  N  N  15.071  18.480  16.402   8.023  -0.150   1.728  HN21    GDP  42  
GDP  HN22    HN22    H  0  0  N  N  N  13.993  17.554  15.413   6.915   1.062   2.086  HN22    GDP  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
GDP  PB     O1B     DOUB  N  N   1  
GDP  PB     O2B     SING  N  N   2  
GDP  PB     O3B     SING  N  N   3  
GDP  PB     O3A     SING  N  N   4  
GDP  O2B    HOB2    SING  N  N   5  
GDP  O3B    HOB3    SING  N  N   6  
GDP  O3A    PA      SING  N  N   7  
GDP  PA     O1A     DOUB  N  N   8  
GDP  PA     O2A     SING  N  N   9  
GDP  PA     "O5'"   SING  N  N  10  
GDP  O2A    HOA2    SING  N  N  11  
GDP  "O5'"  "C5'"   SING  N  N  12  
GDP  "C5'"  "C4'"   SING  N  N  13  
GDP  "C5'"  "H5'"   SING  N  N  14  
GDP  "C5'"  "H5''"  SING  N  N  15  
GDP  "C4'"  "O4'"   SING  N  N  16  
GDP  "C4'"  "C3'"   SING  N  N  17  
GDP  "C4'"  "H4'"   SING  N  N  18  
GDP  "O4'"  "C1'"   SING  N  N  19  
GDP  "C3'"  "O3'"   SING  N  N  20  
GDP  "C3'"  "C2'"   SING  N  N  21  
GDP  "C3'"  "H3'"   SING  N  N  22  
GDP  "O3'"  "HO3'"  SING  N  N  23  
GDP  "C2'"  "O2'"   SING  N  N  24  
GDP  "C2'"  "C1'"   SING  N  N  25  
GDP  "C2'"  "H2'"   SING  N  N  26  
GDP  "O2'"  "HO2'"  SING  N  N  27  
GDP  "C1'"  N9      SING  N  N  28  
GDP  "C1'"  "H1'"   SING  N  N  29  
GDP  N9     C8      SING  Y  N  30  
GDP  N9     C4      SING  Y  N  31  
GDP  C8     N7      DOUB  Y  N  32  
GDP  C8     H8      SING  N  N  33  
GDP  N7     C5      SING  Y  N  34  
GDP  C5     C6      SING  N  N  35  
GDP  C5     C4      DOUB  Y  N  36  
GDP  C6     O6      DOUB  N  N  37  
GDP  C6     N1      SING  N  N  38  
GDP  N1     C2      SING  N  N  39  
GDP  N1     HN1     SING  N  N  40  
GDP  C2     N2      SING  N  N  41  
GDP  C2     N3      DOUB  N  N  42  
GDP  N2     HN21    SING  N  N  43  
GDP  N2     HN22    SING  N  N  44  
GDP  N3     C4      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
GDP  SMILES            ACDLabs               12.01  "O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O"  
GDP  InChI             InChI                 1.03   "InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1"  
GDP  InChIKey          InChI                 1.03   QGWNDRXFNXRZMB-UUOKFMHZSA-N  
GDP  SMILES_CANONICAL  CACTVS                3.385  "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O"  
GDP  SMILES            CACTVS                3.385  "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O"  
GDP  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N"  
GDP  SMILES            "OpenEye OEToolkits"  1.7.6  "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=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
GDP  "SYSTEMATIC NAME"  ACDLabs               12.01  "guanosine 5'-(trihydrogen diphosphate)"  
GDP  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "[(2R,3S,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3,4-bis(oxidanyl)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
GDP  "Create component"    1999-07-08  EBI   
GDP  "Modify descriptor"   2011-06-04  RCSB  
GDP  "Other modification"  2014-05-12  RCSB  
##
