data_GDU
#

_chem_comp.id                                   GDU
_chem_comp.name                                 "GALACTOSE-URIDINE-5'-DIPHOSPHATE"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            ATOMS
_chem_comp.formula                              "C15 H24 N2 O17 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        UDP-D-GALACTOPYRANOSE
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    1999-07-08
_chem_comp.pdbx_modified_date                   2021-03-01
_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                       566.302
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    GDU
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       ?
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       1GUP
_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
GDU  N1      N1      N  0  1  N  N  N  -4.190   -9.628  156.134   0.863  -0.669   5.783  N1      GDU   1  
GDU  C2      C2      C  0  1  N  N  N  -5.510   -9.860  156.451   1.592   0.378   5.358  C2      GDU   2  
GDU  N3      N3      N  0  1  N  N  N  -6.065  -10.955  155.859   2.872   0.532   5.745  N3      GDU   3  
GDU  C4      C4      C  0  1  N  N  N  -5.466  -11.822  154.957   3.449  -0.371   6.561  C4      GDU   4  
GDU  C5      C5      C  0  1  N  N  N  -4.095  -11.515  154.703   2.695  -1.482   7.012  C5      GDU   5  
GDU  C6      C6      C  0  1  N  N  N  -3.512  -10.481  155.269   1.412  -1.610   6.612  C6      GDU   6  
GDU  O2      O2      O  0  1  N  N  N  -6.156   -9.185  157.200   1.085   1.201   4.622  O2      GDU   7  
GDU  O4      O4      O  0  1  N  N  N  -6.143  -12.742  154.506   4.609  -0.235   6.908  O4      GDU   8  
GDU  C1D     C1*     C  0  1  N  N  R  -3.495   -8.478  156.729  -0.528  -0.809   5.349  C1D     GDU   9  
GDU  C2D     C2*     C  0  1  N  N  R  -2.165   -8.841  157.367  -1.344   0.460   5.705  C2D     GDU  10  
GDU  O2D     O2*     O  0  1  N  N  N  -2.299   -9.525  158.654  -1.854   0.381   7.038  O2D     GDU  11  
GDU  C3D     C3*     C  0  1  N  N  S  -1.401   -7.474  157.399  -2.496   0.407   4.668  C3D     GDU  12  
GDU  C4D     C4*     C  0  1  N  N  R  -2.084   -6.710  156.275  -1.950  -0.498   3.548  C4D     GDU  13  
GDU  O4D     O4*     O  0  1  N  N  N  -3.145   -7.541  155.745  -0.608  -0.868   3.909  O4D     GDU  14  
GDU  O3D     O3*     O  0  1  N  N  N  -1.557   -6.694  158.596  -3.669  -0.162   5.253  O3D     GDU  15  
GDU  C5D     C5*     C  0  1  N  N  N  -1.215   -6.035  155.234  -1.940   0.263   2.221  C5D     GDU  16  
GDU  O5D     O5*     O  0  1  N  N  N  -1.017   -4.635  155.581  -1.425  -0.581   1.190  O5D     GDU  17  
GDU  PA      PA      P  0  1  N  N  R   0.448   -3.932  155.456  -1.444   0.279  -0.169  PA      GDU  18  
GDU  O1A     O1A     O  0  1  N  N  N   0.938   -3.981  154.049  -2.832   0.692  -0.473  O1A     GDU  19  
GDU  O2A     O2A     O  0  1  N  N  N   0.462   -2.499  155.839  -0.522   1.587   0.010  O2A     GDU  20  
GDU  O3A     O3A     O  0  1  N  N  N   1.535   -4.658  156.496  -0.874  -0.616  -1.380  O3A     GDU  21  
GDU  PB      PB      P  0  1  N  N  S   1.514   -5.563  157.793  -0.921   0.302  -2.701  PB      GDU  22  
GDU  O1B     O1B     O  0  1  N  N  N   0.306   -5.237  158.610  -2.317   0.715  -2.965  O1B     GDU  23  
GDU  O2B     O2B     O  0  1  N  N  N   1.565   -7.044  157.508  -0.008   1.610  -2.478  O2B     GDU  24  
GDU  O3B     O3B     O  0  1  N  N  N   2.882   -5.263  158.629  -0.361  -0.534  -3.957  O3B     GDU  25  
GDU  "C1'"   "C1'"   C  0  1  N  N  R   3.544   -4.005  158.412  -0.428   0.329  -5.093  "C1'"   GDU  26  
GDU  "C2'"   "C2'"   C  0  1  N  N  R   4.935   -4.060  159.028  -0.656  -0.506  -6.354  "C2'"   GDU  27  
GDU  "C3'"   "C3'"   C  0  1  N  N  S   4.860   -4.413  160.500   0.493  -1.508  -6.503  "C3'"   GDU  28  
GDU  "C4'"   "C4'"   C  0  1  N  N  R   4.159   -3.255  161.204   1.820  -0.742  -6.459  "C4'"   GDU  29  
GDU  "C5'"   "C5'"   C  0  1  N  N  R   2.785   -3.078  160.511   1.861   0.110  -5.188  "C5'"   GDU  30  
GDU  "C6'"   "C6'"   C  0  1  N  N  N   1.986   -1.877  160.984   3.197   0.853  -5.117  "C6'"   GDU  31  
GDU  "O2'"   "O2'"   O  0  1  N  N  N   5.797   -5.026  158.418  -1.895  -1.209  -6.245  "O2'"   GDU  32  
GDU  "O3'"   "O3'"   O  0  1  N  N  N   6.222   -4.533  160.919   0.373  -2.194  -7.751  "O3'"   GDU  33  
GDU  "O4'"   "O4'"   O  0  1  N  N  N   4.864   -2.025  161.064   1.924   0.100  -7.608  "O4'"   GDU  34  
GDU  "O5'"   "O5'"   O  0  1  N  N  N   2.850   -2.940  159.056   0.793   1.056  -5.208  "O5'"   GDU  35  
GDU  "O6'"   "O6'"   O  0  1  N  N  N   2.658   -0.655  160.668   3.237   1.647  -3.930  "O6'"   GDU  36  
GDU  HN3     HN3     H  0  1  N  N  N  -7.032  -11.146  156.118   3.382   1.296   5.432  HN3     GDU  37  
GDU  H5      H5      H  0  1  N  N  N  -3.451  -12.109  154.032   3.141  -2.216   7.666  H5      GDU  38  
GDU  H6      H6      H  0  1  N  N  N  -2.449  -10.328  155.017   0.821  -2.450   6.946  H6      GDU  39  
GDU  H1D     H1*     H  0  1  N  N  N  -4.214   -8.087  157.486  -0.981  -1.694   5.795  H1D     GDU  40  
GDU  H2D     H2*     H  0  1  N  N  N  -1.593   -9.609  156.795  -0.741   1.359   5.573  H2D     GDU  41  
GDU  "HO2'"  *HO2    H  0  0  N  N  N  -1.467   -9.752  159.053  -2.349   1.197   7.196  "HO2'"  GDU  42  
GDU  H3D     H3*     H  0  1  N  N  N  -0.303   -7.654  157.321  -2.709   1.404   4.283  H3D     GDU  43  
GDU  H4D     H4*     H  0  1  N  N  N  -2.508   -5.787  156.734  -2.568  -1.391   3.458  H4D     GDU  44  
GDU  "HO3'"  *HO3    H  0  0  N  N  N  -1.093   -5.864  158.615  -3.927   0.417   5.983  "HO3'"  GDU  45  
GDU  "H5'1"  1H5*    H  0  0  N  N  N  -0.247   -6.569  155.087  -1.310   1.147   2.314  "H5'1"  GDU  46  
GDU  "H5'2"  2H5*    H  0  0  N  N  N  -1.626   -6.156  154.204  -2.956   0.566   1.969  "H5'2"  GDU  47  
GDU  HOA2    2HOA    H  0  0  N  N  N   1.316   -2.089  155.766   0.370   1.274   0.206  HOA2    GDU  48  
GDU  HOB2    2HOB    H  0  0  N  N  N   1.552   -7.587  158.287   0.891   1.297  -2.309  HOB2    GDU  49  
GDU  "H1'"   "H1'"   H  0  1  N  N  N   3.580   -3.826  157.312  -1.255   1.029  -4.967  "H1'"   GDU  50  
GDU  "H2'"   "H2'"   H  0  1  N  N  N   5.356   -3.041  158.863  -0.684   0.148  -7.225  "H2'"   GDU  51  
GDU  "H3'"   "H3'"   H  0  1  N  N  N   4.299   -5.350  160.723   0.458  -2.229  -5.686  "H3'"   GDU  52  
GDU  "H4'"   "H4'"   H  0  1  N  N  N   4.086   -3.491  162.291   2.649  -1.449  -6.448  "H4'"   GDU  53  
GDU  "H5'"   "H5'"   H  0  1  N  N  N   2.284   -4.030  160.802   1.757  -0.534  -4.316  "H5'"   GDU  54  
GDU  "H6'1"  "1H6'"  H  0  0  N  N  N   0.946   -1.890  160.580   3.301   1.498  -5.989  "H6'1"  GDU  55  
GDU  "H6'2"  "2H6'"  H  0  0  N  N  N   1.747   -1.945  162.071   4.013   0.131  -5.099  "H6'2"  GDU  56  
GDU  HO2A    "'HO2"  H  0  0  N  N  N   6.665   -5.060  158.802  -2.587  -0.541  -6.146  HO2A    GDU  57  
GDU  HO3A    "'HO3"  H  0  0  N  N  N   6.175   -4.754  161.841  -0.478  -2.650  -7.739  HO3A    GDU  58  
GDU  "HO4'"  "'HO4"  H  0  0  N  N  N   4.427   -1.304  161.502   1.888  -0.477  -8.382  "HO4'"  GDU  59  
GDU  "HO6'"  "'HO6"  H  0  0  N  N  N   2.158    0.096  160.964   4.093   2.097  -3.923  "HO6'"  GDU  60  
#   #
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
GDU  N1     C2      SING  N  N   1  
GDU  N1     C6      SING  N  N   2  
GDU  N1     C1D     SING  N  N   3  
GDU  C2     N3      SING  N  N   4  
GDU  C2     O2      DOUB  N  N   5  
GDU  N3     C4      SING  N  N   6  
GDU  N3     HN3     SING  N  N   7  
GDU  C4     C5      SING  N  N   8  
GDU  C4     O4      DOUB  N  N   9  
GDU  C5     C6      DOUB  N  N  10  
GDU  C5     H5      SING  N  N  11  
GDU  C6     H6      SING  N  N  12  
GDU  C1D    C2D     SING  N  N  13  
GDU  C1D    O4D     SING  N  N  14  
GDU  C1D    H1D     SING  N  N  15  
GDU  C2D    O2D     SING  N  N  16  
GDU  C2D    C3D     SING  N  N  17  
GDU  C2D    H2D     SING  N  N  18  
GDU  O2D    "HO2'"  SING  N  N  19  
GDU  C3D    C4D     SING  N  N  20  
GDU  C3D    O3D     SING  N  N  21  
GDU  C3D    H3D     SING  N  N  22  
GDU  C4D    O4D     SING  N  N  23  
GDU  C4D    C5D     SING  N  N  24  
GDU  C4D    H4D     SING  N  N  25  
GDU  O3D    "HO3'"  SING  N  N  26  
GDU  C5D    O5D     SING  N  N  27  
GDU  C5D    "H5'1"  SING  N  N  28  
GDU  C5D    "H5'2"  SING  N  N  29  
GDU  O5D    PA      SING  N  N  30  
GDU  PA     O1A     DOUB  N  N  31  
GDU  PA     O2A     SING  N  N  32  
GDU  PA     O3A     SING  N  N  33  
GDU  O2A    HOA2    SING  N  N  34  
GDU  O3A    PB      SING  N  N  35  
GDU  PB     O1B     DOUB  N  N  36  
GDU  PB     O2B     SING  N  N  37  
GDU  PB     O3B     SING  N  N  38  
GDU  O2B    HOB2    SING  N  N  39  
GDU  O3B    "C1'"   SING  N  N  40  
GDU  "C1'"  "C2'"   SING  N  N  41  
GDU  "C1'"  "O5'"   SING  N  N  42  
GDU  "C1'"  "H1'"   SING  N  N  43  
GDU  "C2'"  "C3'"   SING  N  N  44  
GDU  "C2'"  "O2'"   SING  N  N  45  
GDU  "C2'"  "H2'"   SING  N  N  46  
GDU  "C3'"  "C4'"   SING  N  N  47  
GDU  "C3'"  "O3'"   SING  N  N  48  
GDU  "C3'"  "H3'"   SING  N  N  49  
GDU  "C4'"  "C5'"   SING  N  N  50  
GDU  "C4'"  "O4'"   SING  N  N  51  
GDU  "C4'"  "H4'"   SING  N  N  52  
GDU  "C5'"  "C6'"   SING  N  N  53  
GDU  "C5'"  "O5'"   SING  N  N  54  
GDU  "C5'"  "H5'"   SING  N  N  55  
GDU  "C6'"  "O6'"   SING  N  N  56  
GDU  "C6'"  "H6'1"  SING  N  N  57  
GDU  "C6'"  "H6'2"  SING  N  N  58  
GDU  "O2'"  HO2A    SING  N  N  59  
GDU  "O3'"  HO3A    SING  N  N  60  
GDU  "O4'"  "HO4'"  SING  N  N  61  
GDU  "O6'"  "HO6'"  SING  N  N  62  
#   #
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
GDU  SMILES            ACDLabs               10.04  "O=P(OC1OC(C(O)C(O)C1O)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O"  
GDU  SMILES_CANONICAL  CACTVS                3.341  "OC[C@H]1O[C@H](O[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](O)[C@@H](O)[C@H]1O"  
GDU  SMILES            CACTVS                3.341  "OC[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](O)[CH](O)[CH]1O"  
GDU  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@H]([C@H](O3)CO)O)O)O)O)O"  
GDU  SMILES            "OpenEye OEToolkits"  1.5.0  "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)O)O)O"  
GDU  InChI             InChI                 1.03   "InChI=1S/C15H24N2O17P2/c18-3-5-8(20)10(22)12(24)14(32-5)33-36(28,29)34-35(26,27)30-4-6-9(21)11(23)13(31-6)17-2-1-7(19)16-15(17)25/h1-2,5-6,8-14,18,20-24H,3-4H2,(H,26,27)(H,28,29)(H,16,19,25)/t5-,6-,8+,9-,10+,11-,12-,13-,14-/m1/s1"  
GDU  InChIKey          InChI                 1.03   HSCJRCZFDFQWRP-ABVWGUQPSA-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
GDU  "SYSTEMATIC NAME"  ACDLabs               10.04  "[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)"  
GDU  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-phosphoryl] 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
GDU  "Create component"   1999-07-08  PDBJ  
GDU  "Modify descriptor"  2011-06-04  RCSB  
GDU  "Modify synonyms"    2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     GDU
_pdbx_chem_comp_synonyms.name        UDP-D-GALACTOPYRANOSE
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
