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                    2008-10-14 
_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 InChI            InChI                1.02b 
InChI=1/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/f/h16,26,28H 
GDU InChIKey         InChI                1.02b HSCJRCZFDFQWRP-FDIIUVSNDN 
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 
# 
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" 
# 
