data_UD6
#

_chem_comp.id                                   UD6
_chem_comp.name                                 
;[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]
[(2R,3R,4R,5R,6R)-6-(hydroxymethyl)-4,5-bis(oxidanyl)-3-(2-oxidanylidenepropyl)oxan-2-yl] hydrogen phosphate
;

_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C18 H28 N2 O17 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        UDP-2-ketoGlc
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2011-05-11
_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                       606.366
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    UD6
_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       3RUH
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
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
UD6  N1      N1      N  0  1  N  N  N  -24.903  -15.693  43.212  -5.880  -1.015  -0.587  N1      UD6   1  
UD6  C2      C2      C  0  1  N  N  N  -25.765  -15.437  42.132  -5.726  -1.229   0.732  C2      UD6   2  
UD6  O2      O2      O  0  1  N  N  N  -25.890  -14.296  41.679  -5.145  -0.402   1.410  O2      UD6   3  
UD6  N3      N3      N  0  1  N  N  N  -26.493  -16.502  41.578  -6.206  -2.344   1.313  N3      UD6   4  
UD6  C4      C4      C  0  1  N  N  N  -26.356  -17.798  42.089  -6.853  -3.269   0.576  C4      UD6   5  
UD6  O4      O4      O  0  1  N  N  N  -26.996  -18.717  41.591  -7.288  -4.278   1.101  O4      UD6   6  
UD6  C5      C5      C  0  1  N  N  N  -25.502  -18.053  43.156  -7.021  -3.057  -0.813  C5      UD6   7  
UD6  C6      C6      C  0  1  N  N  N  -24.772  -17.010  43.713  -6.530  -1.930  -1.370  C6      UD6   8  
UD6  PA      PA      P  0  1  N  N  N  -20.729  -17.521  46.043  -0.189   1.964   0.861  PA      UD6   9  
UD6  PB      PB      P  0  1  N  N  N  -19.999  -16.123  48.513   2.366   0.493   1.162  PB      UD6  10  
UD6  "C1'"   "C1'"   C  0  1  N  N  R  -18.685  -16.582  50.664   4.755  -0.422   0.391  "C1'"   UD6  11  
UD6  "O1'"   "O1'"   O  0  1  N  N  N  -18.676  -16.535  49.256   3.430  -0.004   0.060  "O1'"   UD6  12  
UD6  O1A     O1A     O  0  1  N  N  N  -21.801  -18.536  46.092   0.260   3.504   0.722  O1A     UD6  13  
UD6  C1B     C1B     C  0  1  N  N  R  -24.125  -14.577  43.808  -5.352   0.211  -1.190  C1B     UD6  14  
UD6  O1B     O1B     O  0  1  N  N  N  -19.713  -14.836  47.836   2.953   1.600   1.950  O1B     UD6  15  
UD6  "C2'"   "C2'"   C  0  1  N  N  R  -17.274  -16.235  51.153   5.694  -0.117  -0.780  "C2'"   UD6  16  
UD6  "O2'"   "O2'"   O  0  1  N  N  N  -25.404  -13.658  45.624  -7.279   1.721  -1.372  "O2'"   UD6  17  
UD6  O2A     O2A     O  0  1  N  N  N  -19.634  -17.674  45.061  -0.559   1.683   2.266  O2A     UD6  18  
UD6  C2B     C2B     C  0  1  N  N  R  -24.276  -14.477  45.324  -6.088   1.456  -0.630  C2B     UD6  19  
UD6  O2B     O2B     O  0  1  N  N  N  -21.152  -16.225  49.439   2.000  -0.729   2.144  O2B     UD6  20  
UD6  "C3'"   "C3'"   C  0  1  N  N  R  -16.316  -17.283  50.607   5.246  -0.919  -2.006  "C3'"   UD6  21  
UD6  "O3'"   "O3'"   O  0  1  N  N  N  -15.035  -17.098  51.197   6.159  -0.697  -3.082  "O3'"   UD6  22  
UD6  O3A     O3A     O  0  1  N  N  N  -20.066  -17.419  47.518   1.030   1.008   0.425  O3A     UD6  23  
UD6  C3B     C3B     C  0  1  N  N  S  -22.982  -13.774  45.723  -5.041   2.576  -0.846  C3B     UD6  24  
UD6  O3B     O3B     O  0  1  N  N  N  -23.176  -12.352  45.720  -5.326   3.302  -2.043  O3B     UD6  25  
UD6  "C4'"   "C4'"   C  0  1  N  N  R  -16.838  -18.705  50.902   5.227  -2.408  -1.649  "C4'"   UD6  26  
UD6  "O4'"   "O4'"   O  0  1  N  N  N  -16.754  -18.968  52.310   6.550  -2.838  -1.322  "O4'"   UD6  27  
UD6  C4B     C4B     C  0  1  N  N  R  -21.999  -14.142  44.597  -3.703   1.822  -0.974  C4B     UD6  28  
UD6  O4B     O4B     O  0  1  N  N  N  -22.740  -14.888  43.617  -3.980   0.424  -0.793  O4B     UD6  29  
UD6  "C5'"   "C5'"   C  0  1  N  N  R  -18.279  -18.927  50.372   4.306  -2.625  -0.445  "C5'"   UD6  30  
UD6  "O5'"   "O5'"   O  0  1  N  N  N  -19.119  -17.925  50.989   4.761  -1.827   0.650  "O5'"   UD6  31  
UD6  C5B     C5B     C  0  1  N  N  N  -20.906  -15.100  45.030  -2.730   2.304   0.105  C5B     UD6  32  
UD6  O5B     O5B     O  0  1  N  N  N  -21.452  -16.104  45.861  -1.456   1.686  -0.093  O5B     UD6  33  
UD6  "C6'"   "C6'"   C  0  1  N  N  N  -18.950  -20.304  50.600   4.328  -4.101  -0.045  "C6'"   UD6  34  
UD6  "O6'"   "O6'"   O  0  1  N  N  N  -18.149  -21.145  51.439   3.382  -4.325   1.003  "O6'"   UD6  35  
UD6  "C7'"   "C7'"   C  0  1  N  N  N  -17.465  -13.655  51.090   6.194   2.160   0.066  "C7'"   UD6  36  
UD6  "O7'"   "O7'"   O  0  1  N  N  N  -18.442  -13.687  51.840   6.586   1.580   1.051  "O7'"   UD6  37  
UD6  "C8'"   "C8'"   C  0  1  N  N  N  -16.942  -12.315  50.578   6.255   3.664   0.004  "C8'"   UD6  38  
UD6  "C9'"   "C9'"   C  0  1  N  N  N  -16.832  -14.832  50.684   5.644   1.379  -1.099  "C9'"   UD6  39  
UD6  H5      H5      H  0  1  N  N  N  -25.407  -19.054  43.549  -7.536  -3.788  -1.420  H5      UD6  40  
UD6  H6      H6      H  0  1  N  N  N  -24.099  -17.206  44.535  -6.653  -1.749  -2.428  H6      UD6  41  
UD6  "H1'"   "H1'"   H  0  1  N  N  N  -19.359  -15.864  51.154   5.095   0.113   1.278  "H1'"   UD6  42  
UD6  HO1A    HO1A    H  0  0  N  N  N  -21.635  -19.204  45.438   0.516   3.759  -0.175  HO1A    UD6  43  
UD6  H1B     H1B     H  0  1  N  N  N  -24.479  -13.648  43.337  -5.438   0.171  -2.276  H1B     UD6  44  
UD6  "H2'"   "H2'"   H  0  1  N  N  N  -17.269  -16.228  52.253   6.713  -0.398  -0.513  "H2'"   UD6  45  
UD6  "HO2'"  "HO2'"  H  0  0  N  N  N  -25.505  -13.590  46.566  -7.774   2.490  -1.060  "HO2'"  UD6  46  
UD6  H2B     H2B     H  0  1  N  N  N  -24.430  -15.436  45.840  -6.311   1.331   0.430  H2B     UD6  47  
UD6  HO2B    HO2B    H  0  0  N  N  N  -21.597  -15.387  49.485   1.611  -1.492   1.695  HO2B    UD6  48  
UD6  "H3'"   "H3'"   H  0  1  N  N  N  -16.240  -17.167  49.516   4.246  -0.602  -2.303  "H3'"   UD6  49  
UD6  "HO3'"  "HO3'"  H  0  0  N  N  N  -14.433  -17.750  50.859   5.936  -1.175  -3.892  "HO3'"  UD6  50  
UD6  H3B     H3B     H  0  1  N  N  N  -22.635  -14.067  46.725  -5.020   3.248   0.012  H3B     UD6  51  
UD6  HO3B    HO3B    H  0  0  N  N  N  -22.367  -11.921  45.969  -6.183   3.748  -2.038  HO3B    UD6  52  
UD6  "H4'"   "H4'"   H  0  1  N  N  N  -16.199  -19.420  50.363   4.857  -2.981  -2.499  "H4'"   UD6  53  
UD6  "HO4'"  "HO4'"  H  0  0  N  N  N  -17.076  -19.844  52.489   6.612  -3.773  -1.085  "HO4'"  UD6  54  
UD6  H4B     H4B     H  0  1  N  N  N  -21.551  -13.199  44.250  -3.275   1.993  -1.962  H4B     UD6  55  
UD6  "H5'"   "H5'"   H  0  1  N  N  N  -18.177  -18.864  49.279   3.289  -2.335  -0.708  "H5'"   UD6  56  
UD6  H5B     H5B     H  0  1  N  N  N  -20.457  -15.567  44.141  -2.622   3.386   0.040  H5B     UD6  57  
UD6  H5BA    H5BA    H  0  0  N  N  N  -20.135  -14.546  45.585  -3.115   2.034   1.088  H5BA    UD6  58  
UD6  "H6'"   "H6'"   H  0  1  N  N  N  -19.926  -20.147  51.083   4.068  -4.715  -0.907  "H6'"   UD6  59  
UD6  "H6'A"  "H6'A"  H  0  0  N  N  N  -19.084  -20.799  49.627   5.326  -4.368   0.304  "H6'A"  UD6  60  
UD6  "HO6'"  "HO6'"  H  0  0  N  N  N  -18.585  -21.980  51.560   3.342  -5.242   1.307  "HO6'"  UD6  61  
UD6  "H8'"   "H8'"   H  0  1  N  N  N  -17.560  -11.500  50.983   6.679   4.050   0.931  "H8'"   UD6  62  
UD6  "H8'A"  "H8'A"  H  0  0  N  N  N  -15.900  -12.180  50.903   6.881   3.967  -0.836  "H8'A"  UD6  63  
UD6  "H8'B"  "H8'B"  H  0  0  N  N  N  -16.989  -12.299  49.479   5.250   4.063  -0.130  "H8'B"  UD6  64  
UD6  "H9'"   "H9'"   H  0  1  N  N  N  -15.791  -14.730  51.025   6.243   1.581  -1.987  "H9'"   UD6  65  
UD6  "H9'A"  "H9'A"  H  0  0  N  N  N  -16.934  -14.850  49.589   4.611   1.677  -1.281  "H9'A"  UD6  66  
UD6  HN3     HN3     H  0  1  N  N  N  -27.114  -16.333  40.813  -6.087  -2.482   2.266  HN3     UD6  67  
#   #
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
UD6  C2     N1      SING  N  N   1  
UD6  N1     C6      SING  N  N   2  
UD6  N1     C1B     SING  N  N   3  
UD6  N3     C2      SING  N  N   4  
UD6  O2     C2      DOUB  N  N   5  
UD6  N3     C4      SING  N  N   6  
UD6  O4     C4      DOUB  N  N   7  
UD6  C4     C5      SING  N  N   8  
UD6  C5     C6      DOUB  N  N   9  
UD6  C5     H5      SING  N  N  10  
UD6  C6     H6      SING  N  N  11  
UD6  O2A    PA      DOUB  N  N  12  
UD6  O5B    PA      SING  N  N  13  
UD6  PA     O1A     SING  N  N  14  
UD6  PA     O3A     SING  N  N  15  
UD6  O3A    PB      SING  N  N  16  
UD6  O1B    PB      DOUB  N  N  17  
UD6  PB     "O1'"   SING  N  N  18  
UD6  PB     O2B     SING  N  N  19  
UD6  "O1'"  "C1'"   SING  N  N  20  
UD6  "C1'"  "O5'"   SING  N  N  21  
UD6  "C1'"  "C2'"   SING  N  N  22  
UD6  "C1'"  "H1'"   SING  N  N  23  
UD6  O1A    HO1A    SING  N  N  24  
UD6  O4B    C1B     SING  N  N  25  
UD6  C1B    C2B     SING  N  N  26  
UD6  C1B    H1B     SING  N  N  27  
UD6  "C3'"  "C2'"   SING  N  N  28  
UD6  "C9'"  "C2'"   SING  N  N  29  
UD6  "C2'"  "H2'"   SING  N  N  30  
UD6  C2B    "O2'"   SING  N  N  31  
UD6  "O2'"  "HO2'"  SING  N  N  32  
UD6  C2B    C3B     SING  N  N  33  
UD6  C2B    H2B     SING  N  N  34  
UD6  O2B    HO2B    SING  N  N  35  
UD6  "C3'"  "C4'"   SING  N  N  36  
UD6  "C3'"  "O3'"   SING  N  N  37  
UD6  "C3'"  "H3'"   SING  N  N  38  
UD6  "O3'"  "HO3'"  SING  N  N  39  
UD6  C4B    C3B     SING  N  N  40  
UD6  O3B    C3B     SING  N  N  41  
UD6  C3B    H3B     SING  N  N  42  
UD6  O3B    HO3B    SING  N  N  43  
UD6  "C5'"  "C4'"   SING  N  N  44  
UD6  "C4'"  "O4'"   SING  N  N  45  
UD6  "C4'"  "H4'"   SING  N  N  46  
UD6  "O4'"  "HO4'"  SING  N  N  47  
UD6  O4B    C4B     SING  N  N  48  
UD6  C4B    C5B     SING  N  N  49  
UD6  C4B    H4B     SING  N  N  50  
UD6  "C5'"  "C6'"   SING  N  N  51  
UD6  "C5'"  "O5'"   SING  N  N  52  
UD6  "C5'"  "H5'"   SING  N  N  53  
UD6  C5B    O5B     SING  N  N  54  
UD6  C5B    H5B     SING  N  N  55  
UD6  C5B    H5BA    SING  N  N  56  
UD6  "C6'"  "O6'"   SING  N  N  57  
UD6  "C6'"  "H6'"   SING  N  N  58  
UD6  "C6'"  "H6'A"  SING  N  N  59  
UD6  "O6'"  "HO6'"  SING  N  N  60  
UD6  "C8'"  "C7'"   SING  N  N  61  
UD6  "C9'"  "C7'"   SING  N  N  62  
UD6  "C7'"  "O7'"   DOUB  N  N  63  
UD6  "C8'"  "H8'"   SING  N  N  64  
UD6  "C8'"  "H8'A"  SING  N  N  65  
UD6  "C8'"  "H8'B"  SING  N  N  66  
UD6  "C9'"  "H9'"   SING  N  N  67  
UD6  "C9'"  "H9'A"  SING  N  N  68  
UD6  N3     HN3     SING  N  N  69  
#   #
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
UD6  SMILES            ACDLabs               12.01  "O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3CC(=O)C)CO)O)O"  
UD6  SMILES_CANONICAL  CACTVS                3.370  "CC(=O)C[C@@H]1[C@@H](O)[C@@H](O)[C@@H](CO)O[C@@H]1O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O"  
UD6  SMILES            CACTVS                3.370  "CC(=O)C[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O"  
UD6  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.2  "CC(=O)C[C@@H]1[C@H]([C@H]([C@H](O[C@@H]1OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)CO)O)O"  
UD6  SMILES            "OpenEye OEToolkits"  1.7.2  "CC(=O)CC1C(C(C(OC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)O)O"  
UD6  InChI             InChI                 1.03   "InChI=1S/C18H28N2O17P2/c1-7(22)4-8-12(24)13(25)9(5-21)35-17(8)36-39(31,32)37-38(29,30)33-6-10-14(26)15(27)16(34-10)20-3-2-11(23)19-18(20)28/h2-3,8-10,12-17,21,24-27H,4-6H2,1H3,(H,29,30)(H,31,32)(H,19,23,28)/t8-,9-,10-,12-,13+,14-,15-,16-,17-/m1/s1"  
UD6  InChIKey          InChI                 1.03   ODPRJDNNGDXFOQ-YIUJVFLPSA-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
UD6  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2R,3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-(2-oxopropyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)"  
UD6  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.2  "[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R,6R)-6-(hydroxymethyl)-4,5-bis(oxidanyl)-3-(2-oxidanylidenepropyl)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
UD6  "Create component"   2011-05-11  RCSB  
UD6  "Modify descriptor"  2011-06-04  RCSB  
UD6  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     UD6
_pdbx_chem_comp_synonyms.name        UDP-2-ketoGlc
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
