data_GDG
#

_chem_comp.id                                   GDG
_chem_comp.name                                 GDP-ALPHA-D-GLUCOSE
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C16 H25 N5 O16 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        GDP-ALPHA-D-GLUCOSE
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2006-09-05
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       605.341
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    GDG
_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       5K42
_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
GDG  C21  C1   C  0  1  N  N  R  164.955  118.572  36.676   5.981  -0.173  -0.644  C21  GDG   1  
GDG  C22  C2   C  0  1  N  N  R  165.849  117.380  37.067   6.247  -1.113  -1.823  C22  GDG   2  
GDG  C24  C3   C  0  1  N  N  S  165.050  116.102  35.052   5.913  -3.033  -0.265  C24  GDG   3  
GDG  C01  C4   C  0  1  Y  N  N  170.171  122.987  28.693  -4.468  -0.786   1.614  C01  GDG   4  
GDG  N02  N1   N  0  1  Y  N  N  170.879  124.057  28.299  -5.246  -1.758   1.997  N02  GDG   5  
GDG  C03  C5   C  0  1  Y  N  N  170.187  124.699  27.312  -6.146  -2.016   1.020  C03  GDG   6  
GDG  C04  C6   C  0  1  Y  N  N  169.010  123.966  27.116  -5.891  -1.136  -0.024  C04  GDG   7  
GDG  N05  N2   N  0  1  Y  N  N  169.048  122.926  27.981  -4.838  -0.369   0.369  N05  GDG   8  
GDG  C06  C7   C  0  1  N  N  R  167.984  121.968  28.065  -4.210   0.704  -0.407  C06  GDG   9  
GDG  C07  C8   C  0  1  N  N  R  168.384  120.760  27.850  -4.925   2.047  -0.143  C07  GDG  10  
GDG  C08  C9   C  0  1  N  N  S  167.359  119.955  28.583  -3.782   3.087  -0.141  C08  GDG  11  
GDG  C09  C10  C  0  1  N  N  R  167.039  120.840  29.822  -2.512   2.249  -0.405  C09  GDG  12  
GDG  O10  O1   O  0  1  N  N  N  167.378  122.013  29.547  -2.852   0.916   0.036  O10  GDG  13  
GDG  C11  C11  C  0  1  N  N  N  167.885  120.326  31.022  -1.336   2.794   0.408  C11  GDG  14  
GDG  O12  O2   O  0  1  N  N  N  167.257  119.107  31.351  -0.147   2.080   0.064  O12  GDG  15  
GDG  P13  P1   P  0  1  N  N  N  167.620  118.391  32.724   1.286   2.392   0.728  P13  GDG  16  
GDG  O14  O3   O  0  1  N  N  N  167.425  116.919  32.497   1.612   3.825   0.551  O14  GDG  17  
GDG  O15  O4   O  0  1  N  N  N  169.033  118.707  33.111   1.237   2.043   2.299  O15  GDG  18  
GDG  O16  O5   O  0  1  N  N  N  166.620  118.877  33.875   2.415   1.493   0.014  O16  GDG  19  
GDG  P17  P2   P  0  1  N  N  N  166.923  119.797  35.156   4.024   1.536  -0.018  P17  GDG  20  
GDG  O18  O6   O  0  1  N  N  N  167.154  121.212  34.693   4.540   1.752   1.353  O18  GDG  21  
GDG  O19  O7   O  0  1  N  N  N  168.154  119.335  35.941   4.510   2.741  -0.969  O19  GDG  22  
GDG  O20  O8   O  0  1  N  N  N  165.607  119.741  36.123   4.588   0.140  -0.589  O20  GDG  23  
GDG  C23  C12  C  0  1  N  N  S  166.217  116.491  35.893   5.484  -2.423  -1.603  C23  GDG  24  
GDG  C25  C13  C  0  1  N  N  R  164.144  117.281  34.675   5.660  -2.019   0.853  C25  GDG  25  
GDG  O26  O9   O  0  1  N  N  N  163.807  118.167  35.834   6.373  -0.813   0.572  O26  GDG  26  
GDG  C27  C14  C  0  1  N  N  N  162.869  116.820  34.094   6.142  -2.598   2.185  C27  GDG  27  
GDG  O28  O10  O  0  1  N  N  N  162.070  116.205  35.084   5.800  -1.702   3.245  O28  GDG  28  
GDG  O29  O11  O  0  1  N  N  N  165.539  115.476  33.854   5.157  -4.219  -0.016  O29  GDG  29  
GDG  O30  O12  O  0  1  N  N  N  166.862  115.270  36.360   5.785  -3.334  -2.662  O30  GDG  30  
GDG  O31  O13  O  0  1  N  N  N  166.981  117.861  37.763   5.802  -0.498  -3.033  O31  GDG  31  
GDG  O32  O14  O  0  1  N  N  N  166.219  119.764  27.854  -3.975   4.045  -1.184  O32  GDG  32  
GDG  O33  O15  O  0  1  N  N  N  168.374  120.469  26.363  -5.859   2.331  -1.187  O33  GDG  33  
GDG  N34  N3   N  0  1  N  N  N  168.017  124.354  26.130  -6.675  -1.196  -1.148  N34  GDG  34  
GDG  C35  C15  C  0  1  N  N  N  168.249  125.550  25.311  -7.686  -2.099  -1.237  C35  GDG  35  
GDG  N36  N4   N  0  1  N  N  N  169.446  126.300  25.515  -7.961  -2.950  -0.271  N36  GDG  36  
GDG  C37  C16  C  0  1  N  N  N  170.417  125.923  26.469  -7.250  -2.969   0.867  C37  GDG  37  
GDG  O38  O16  O  0  1  N  N  N  171.419  126.596  26.595  -7.516  -3.763   1.755  O38  GDG  38  
GDG  N39  N5   N  0  1  N  N  N  167.317  125.960  24.353  -8.446  -2.126  -2.375  N39  GDG  39  
GDG  H1   H1   H  0  1  N  N  N  164.511  118.906  37.625   6.555   0.744  -0.774  H1   GDG  40  
GDG  H2   H2   H  0  1  N  N  N  165.260  116.762  37.761   7.315  -1.319  -1.890  H2   GDG  41  
GDG  H3   H3   H  0  1  N  N  N  164.443  115.377  35.615   6.975  -3.279  -0.301  H3   GDG  42  
GDG  H4   H4   H  0  1  N  N  N  170.465  122.289  29.463  -3.657  -0.372   2.194  H4   GDG  43  
GDG  H5   H5   H  0  1  N  N  N  167.178  122.257  27.374  -4.230   0.464  -1.470  H5   GDG  44  
GDG  H6   H6   H  0  1  N  N  N  169.384  120.555  28.260  -5.427   2.030   0.825  H6   GDG  45  
GDG  H7   H7   H  0  1  N  N  N  167.797  119.004  28.920  -3.719   3.583   0.827  H7   GDG  46  
GDG  H8   H8   H  0  1  N  N  N  165.972  120.735  30.068  -2.270   2.249  -1.467  H8   GDG  47  
GDG  H9   H9   H  0  1  N  N  N  168.932  120.165  30.727  -1.201   3.853   0.186  H9   GDG  48  
GDG  H10  H10  H  0  1  N  N  N  167.846  121.032  31.865  -1.540   2.669   1.472  H10  GDG  49  
GDG  H11  H11  H  0  1  N  N  N  169.541  117.905  33.139   1.028   1.118   2.490  H11  GDG  50  
GDG  H12  H12  H  0  1  N  N  N  168.795  120.036  35.967   4.208   2.665  -1.885  H12  GDG  51  
GDG  H13  H13  H  0  1  N  N  N  166.927  117.044  35.261   4.413  -2.223  -1.586  H13  GDG  52  
GDG  H14  H14  H  0  1  N  N  N  164.673  117.884  33.923   4.593  -1.804   0.915  H14  GDG  53  
GDG  H15  H15  H  0  1  N  N  N  162.329  117.682  33.676   5.664  -3.562   2.357  H15  GDG  54  
GDG  H16  H16  H  0  1  N  N  N  163.077  116.094  33.294   7.223  -2.729   2.155  H16  GDG  55  
GDG  H17  H17  H  0  1  N  N  N  161.253  115.913  34.696   6.076  -2.006   4.121  H17  GDG  56  
GDG  H18  H18  H  0  1  N  N  N  166.186  116.038  33.444   5.266  -4.904  -0.690  H18  GDG  57  
GDG  H19  H19  H  0  1  N  N  N  167.611  115.494  36.900   5.539  -3.012  -3.540  H19  GDG  58  
GDG  H20  H20  H  0  1  N  N  N  166.699  118.410  38.485   6.240   0.340  -3.233  H20  GDG  59  
GDG  H21  H21  H  0  1  N  N  N  165.601  119.249  28.360  -4.790   4.558  -1.101  H21  GDG  60  
GDG  H22  H22  H  0  1  N  N  N  168.669  119.579  26.212  -6.336   3.164  -1.072  H22  GDG  61  
GDG  H23  H23  H  0  1  N  N  N  167.185  123.813  26.010  -6.507  -0.587  -1.884  H23  GDG  62  
GDG  H24  H24  H  0  1  N  N  N  167.488  126.781  23.808  -9.172  -2.764  -2.458  H24  GDG  63  
GDG  H25  H25  H  0  1  N  N  N  166.479  125.432  24.212  -8.259  -1.508  -3.098  H25  GDG  64  
#   #
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
GDG  N39  C35  SING  N  N   1  
GDG  C35  N36  DOUB  N  N   2  
GDG  C35  N34  SING  N  N   3  
GDG  N36  C37  SING  N  N   4  
GDG  N34  C04  SING  N  N   5  
GDG  O33  C07  SING  N  N   6  
GDG  C37  O38  DOUB  N  N   7  
GDG  C37  C03  SING  N  N   8  
GDG  C04  C03  DOUB  Y  N   9  
GDG  C04  N05  SING  Y  N  10  
GDG  C03  N02  SING  Y  N  11  
GDG  C07  C06  SING  N  N  12  
GDG  C07  C08  SING  N  N  13  
GDG  O32  C08  SING  N  N  14  
GDG  N05  C06  SING  N  N  15  
GDG  N05  C01  SING  Y  N  16  
GDG  C06  O10  SING  N  N  17  
GDG  N02  C01  DOUB  Y  N  18  
GDG  C08  C09  SING  N  N  19  
GDG  O10  C09  SING  N  N  20  
GDG  C09  C11  SING  N  N  21  
GDG  C11  O12  SING  N  N  22  
GDG  O12  P13  SING  N  N  23  
GDG  O14  P13  DOUB  N  N  24  
GDG  P13  O15  SING  N  N  25  
GDG  P13  O16  SING  N  N  26  
GDG  O29  C24  SING  N  N  27  
GDG  O16  P17  SING  N  N  28  
GDG  C27  C25  SING  N  N  29  
GDG  C27  O28  SING  N  N  30  
GDG  C25  C24  SING  N  N  31  
GDG  C25  O26  SING  N  N  32  
GDG  O18  P17  DOUB  N  N  33  
GDG  C24  C23  SING  N  N  34  
GDG  P17  O19  SING  N  N  35  
GDG  P17  O20  SING  N  N  36  
GDG  O26  C21  SING  N  N  37  
GDG  C23  O30  SING  N  N  38  
GDG  C23  C22  SING  N  N  39  
GDG  O20  C21  SING  N  N  40  
GDG  C21  C22  SING  N  N  41  
GDG  C22  O31  SING  N  N  42  
GDG  C21  H1   SING  N  N  43  
GDG  C22  H2   SING  N  N  44  
GDG  C24  H3   SING  N  N  45  
GDG  C01  H4   SING  N  N  46  
GDG  C06  H5   SING  N  N  47  
GDG  C07  H6   SING  N  N  48  
GDG  C08  H7   SING  N  N  49  
GDG  C09  H8   SING  N  N  50  
GDG  C11  H9   SING  N  N  51  
GDG  C11  H10  SING  N  N  52  
GDG  O15  H11  SING  N  N  53  
GDG  O19  H12  SING  N  N  54  
GDG  C23  H13  SING  N  N  55  
GDG  C25  H14  SING  N  N  56  
GDG  C27  H15  SING  N  N  57  
GDG  C27  H16  SING  N  N  58  
GDG  O28  H17  SING  N  N  59  
GDG  O29  H18  SING  N  N  60  
GDG  O30  H19  SING  N  N  61  
GDG  O31  H20  SING  N  N  62  
GDG  O32  H21  SING  N  N  63  
GDG  O33  H22  SING  N  N  64  
GDG  N34  H23  SING  N  N  65  
GDG  N39  H24  SING  N  N  66  
GDG  N39  H25  SING  N  N  67  
#   #
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
GDG  SMILES            ACDLabs               12.01  "C1(C(O)C(C(C(O1)CO)O)O)OP(OP(OCC4C(C(C(n2cnc3c2NC(=NC3=O)N)O4)O)O)(O)=O)(O)=O"  
GDG  InChI             InChI                 1.03   "InChI=1S/C16H25N5O16P2/c17-16-19-12-6(13(28)20-16)18-3-21(12)14-10(26)8(24)5(34-14)2-33-38(29,30)37-39(31,32)36-15-11(27)9(25)7(23)4(1-22)35-15/h3-5,7-11,14-15,22-27H,1-2H2,(H,29,30)(H,31,32)(H3,17,19,20,28)/t4-,5-,7-,8-,9+,10-,11-,14-,15-/m1/s1"  
GDG  InChIKey          InChI                 1.03   MVMSCBBUIHUTGJ-LRJDVEEWSA-N  
GDG  SMILES_CANONICAL  CACTVS                3.385  "NC1=NC(=O)c2ncn([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[C@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4O)[C@@H](O)[C@H]3O)c2N1"  
GDG  SMILES            CACTVS                3.385  "NC1=NC(=O)c2ncn([CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]4O[CH](CO)[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O)c2N1"  
GDG  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.4  "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O[C@@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O)O)O)NC(=NC2=O)N"  
GDG  SMILES            "OpenEye OEToolkits"  2.0.4  "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)CO)O)O)O)O)O)NC(=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
GDG  "SYSTEMATIC NAME"  ACDLabs               12.01  "[(2R,3S,4R,5R)-5-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)"  
GDG  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.4  "[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl] 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
GDG  "Create component"    2006-09-05  EBI   
GDG  "Modify descriptor"   2011-06-04  RCSB  
GDG  "Other modification"  2016-05-21  EBI   
GDG  "Initial release"     2017-06-21  RCSB  
GDG  "Modify synonyms"     2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     GDG
_pdbx_chem_comp_synonyms.name        GDP-ALPHA-D-GLUCOSE
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
