data_UD4
#

_chem_comp.id                                   UD4
_chem_comp.name                                 "UDP-2-acetamido-4-amino-2,4,6-trideoxy-alpha-D-glucopyranose"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C17 H28 N4 O15 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "(2R,3R,4S,5S,6R)-3-(acetylamino)-5-amino-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2008-05-21
_chem_comp.pdbx_modified_date                   2021-03-13
_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                       590.370
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    UD4
_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       3BSS
_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
UD4  N3      N3      N  0  1  N  N  N   3.991  -39.279  -11.483  -6.747  -2.999  -0.873  N3      UD4   1  
UD4  C2      C2      C  0  1  N  N  N   4.357  -38.129  -12.070  -6.271  -1.808  -1.279  C2      UD4   2  
UD4  N1      N1      N  0  1  N  N  N   3.592  -37.631  -13.145  -5.643  -0.985  -0.420  N1      UD4   3  
UD4  C4      C4      C  0  1  N  N  N   2.914  -39.964  -11.916  -6.606  -3.385   0.412  C4      UD4   4  
UD4  C5      C5      C  0  1  N  N  N   2.139  -39.500  -12.976  -5.946  -2.529   1.326  C5      UD4   5  
UD4  C6      C6      C  0  1  N  N  N   2.508  -38.303  -13.590  -5.473  -1.342   0.890  C6      UD4   6  
UD4  "O7'"   "O7'"   O  0  1  N  N  N  -3.400  -31.496  -20.671   7.161   1.208  -1.675  "O7'"   UD4   7  
UD4  "C7'"   "C7'"   C  0  1  N  N  N  -2.254  -31.292  -20.283   6.166   1.044  -2.350  "C7'"   UD4   8  
UD4  "C8'"   "C8'"   C  0  1  N  N  N  -1.042  -31.645  -21.120   5.894   1.950  -3.524  "C8'"   UD4   9  
UD4  "N2'"   "N2'"   N  0  1  N  N  N  -2.006  -30.730  -19.096   5.305   0.052  -2.051  "N2'"   UD4  10  
UD4  "C2'"   "C2'"   C  0  1  N  N  R  -3.047  -30.367  -18.143   5.569  -0.828  -0.910  "C2'"   UD4  11  
UD4  "C3'"   "C3'"   C  0  1  N  N  S  -3.181  -28.839  -18.026   4.869  -2.173  -1.128  "C3'"   UD4  12  
UD4  "O3'"   "O3'"   O  0  1  N  N  N  -3.634  -28.286  -19.274   5.417  -2.816  -2.280  "O3'"   UD4  13  
UD4  "C4'"   "C4'"   C  0  1  N  N  S  -4.127  -28.423  -16.877   5.087  -3.056   0.105  "C4'"   UD4  14  
UD4  N4A     N4A     N  0  1  N  N  N  -4.114  -26.963  -16.726   4.358  -4.320  -0.062  N4A     UD4  15  
UD4  "C5'"   "C5'"   C  0  1  N  N  R  -3.726  -29.125  -15.571   4.568  -2.325   1.345  "C5'"   UD4  16  
UD4  "C6'"   "C6'"   C  0  1  N  N  N  -4.719  -28.910  -14.423   4.837  -3.174   2.589  "C6'"   UD4  17  
UD4  "O5'"   "O5'"   O  0  1  N  N  N  -3.617  -30.546  -15.773   5.238  -1.069   1.472  "O5'"   UD4  18  
UD4  "C1'"   "C1'"   C  0  1  N  N  R  -2.713  -30.984  -16.788   5.031  -0.183   0.370  "C1'"   UD4  19  
UD4  "O1'"   "O1'"   O  0  1  N  N  N  -1.403  -30.569  -16.414   3.633   0.075   0.222  "O1'"   UD4  20  
UD4  PB      PB      P  0  1  N  N  R  -0.374  -31.617  -15.770   2.883   1.293   0.961  PB      UD4  21  
UD4  O2B     O2B     O  0  1  N  N  N   0.922  -30.891  -15.584   3.125   1.209   2.419  O2B     UD4  22  
UD4  O1B     O1B     O  0  1  N  N  N  -1.062  -32.244  -14.577   3.451   2.692   0.402  O1B     UD4  23  
UD4  O3A     O3A     O  0  1  N  N  N  -0.402  -32.752  -16.919   1.301   1.203   0.674  O3A     UD4  24  
UD4  PA      PA      P  0  1  N  N  R   0.777  -33.431  -17.798   0.004   1.890   1.334  PA      UD4  25  
UD4  O2A     O2A     O  0  1  N  N  N   0.203  -34.754  -18.202  -0.307   1.198   2.753  O2A     UD4  26  
UD4  O1A     O1A     O  0  1  N  N  N   1.265  -32.397  -18.789   0.259   3.334   1.535  O1A     UD4  27  
UD4  O5B     O5B     O  0  1  N  N  N   1.933  -33.684  -16.709  -1.261   1.700   0.356  O5B     UD4  28  
UD4  C5B     C5B     C  0  1  N  N  N   1.738  -34.497  -15.540  -2.538   2.288   0.611  C5B     UD4  29  
UD4  C4B     C4B     C  0  1  N  N  R   3.094  -34.571  -14.865  -3.507   1.909  -0.511  C4B     UD4  30  
UD4  O4B     O4B     O  0  1  N  N  N   2.966  -35.421  -13.724  -3.764   0.495  -0.477  O4B     UD4  31  
UD4  C2B     C2B     C  0  1  N  N  S   4.126  -35.205  -15.819  -4.856   2.625  -0.302  C2B     UD4  32  
UD4  O3B     O3B     O  0  1  N  N  N   5.347  -34.452  -15.810  -5.153   3.467  -1.418  O3B     UD4  33  
UD4  C3B     C3B     C  0  1  N  N  R   4.318  -36.600  -15.253  -5.885   1.473  -0.203  C3B     UD4  34  
UD4  "O2'"   "O2'"   O  0  1  N  N  N   5.617  -37.151  -15.502  -7.083   1.798  -0.911  "O2'"   UD4  35  
UD4  C1B     C1B     C  0  1  N  N  R   4.018  -36.387  -13.764  -5.134   0.306  -0.892  C1B     UD4  36  
UD4  O2      O2      O  0  1  N  N  N   5.361  -37.484  -11.674  -6.411  -1.470  -2.439  O2      UD4  37  
UD4  O4      O4      O  0  1  N  N  N   2.596  -41.038  -11.347  -7.041  -4.461   0.781  O4      UD4  38  
UD4  H5      H5      H  0  1  N  N  N   1.275  -40.053  -13.314  -5.824  -2.821   2.358  H5      UD4  39  
UD4  H6      H6      H  0  1  N  N  N   1.930  -37.916  -14.416  -4.968  -0.676   1.573  H6      UD4  40  
UD4  "H8'"   "H8'"   H  0  1  N  N  N  -1.337  -31.731  -22.176   6.695   2.685  -3.608  "H8'"   UD4  41  
UD4  "H8'A"  "H8'A"  H  0  0  N  N  N  -0.282  -30.857  -21.015   5.848   1.357  -4.437  "H8'A"  UD4  42  
UD4  "H8'B"  "H8'B"  H  0  0  N  N  N  -0.627  -32.604  -20.777   4.944   2.463  -3.374  "H8'B"  UD4  43  
UD4  "HN2'"  "HN2'"  H  0  0  N  N  N  -1.054  -30.549  -18.848   4.509  -0.079  -2.590  "HN2'"  UD4  44  
UD4  "H2'"   "H2'"   H  0  1  N  N  N  -4.013  -30.755  -18.497   6.643  -0.988  -0.814  "H2'"   UD4  45  
UD4  "H3'"   "H3'"   H  0  1  N  N  N  -2.185  -28.436  -17.789   3.801  -2.009  -1.274  "H3'"   UD4  46  
UD4  "HO3'"  "HO3'"  H  0  0  N  N  N  -3.734  -27.345  -19.186   5.019  -3.675  -2.478  "HO3'"  UD4  47  
UD4  "H4'"   "H4'"   H  0  1  N  N  N  -5.153  -28.735  -17.121   6.151  -3.262   0.221  "H4'"   UD4  48  
UD4  HN4A    HN4A    H  0  0  N  N  N  -4.111  -26.728  -15.754   4.487  -4.920   0.740  HN4A    UD4  49  
UD4  HN4B    HN4B    H  0  0  N  N  N  -3.295  -26.590  -17.161   3.378  -4.152  -0.234  HN4B    UD4  50  
UD4  "H5'"   "H5'"   H  0  1  N  N  N  -2.762  -28.674  -15.291   3.496  -2.156   1.245  "H5'"   UD4  51  
UD4  "H6'"   "H6'"   H  0  1  N  N  N  -4.173  -28.859  -13.470   5.909  -3.342   2.689  "H6'"   UD4  52  
UD4  "H6'A"  "H6'A"  H  0  0  N  N  N  -5.266  -27.969  -14.583   4.467  -2.654   3.472  "H6'A"  UD4  53  
UD4  "H6'B"  "H6'B"  H  0  0  N  N  N  -5.431  -29.748  -14.392   4.326  -4.133   2.491  "H6'B"  UD4  54  
UD4  "H1'"   "H1'"   H  0  1  N  N  N  -2.787  -32.078  -16.881   5.556   0.754   0.553  "H1'"   UD4  55  
UD4  HO1B    HO1B    H  0  0  N  N  N  -0.430  -32.375  -13.880   3.327   2.815  -0.549  HO1B    UD4  56  
UD4  HO2A    HO2A    H  0  0  N  N  N   0.081  -34.773  -19.144  -0.484   0.249   2.698  HO2A    UD4  57  
UD4  H5B     H5B     H  0  1  N  N  N   0.992  -34.045  -14.870  -2.922   1.923   1.563  H5B     UD4  58  
UD4  H5BA    H5BA    H  0  0  N  N  N   1.359  -35.496  -15.800  -2.436   3.373   0.652  H5BA    UD4  59  
UD4  H4B     H4B     H  0  1  N  N  N   3.426  -33.560  -14.585  -3.083   2.185  -1.476  H4B     UD4  60  
UD4  H2B     H2B     H  0  1  N  N  N   3.801  -35.223  -16.870  -4.840   3.206   0.620  H2B     UD4  61  
UD4  HO3B    HO3B    H  0  0  N  N  N   5.624  -34.286  -16.703  -5.991   3.943  -1.339  HO3B    UD4  62  
UD4  H3B     H3B     H  0  1  N  N  N   3.667  -37.350  -15.725  -6.103   1.235   0.838  H3B     UD4  63  
UD4  "HO2'"  "HO2'"  H  0  0  N  N  N   5.736  -37.273  -16.437  -7.542   2.579  -0.572  "HO2'"  UD4  64  
UD4  H1B     H1B     H  0  1  N  N  N   4.907  -36.047  -13.213  -5.223   0.379  -1.976  H1B     UD4  65  
UD4  HN3     HN3     H  0  1  N  N  N   4.524  -39.632  -10.714  -7.198  -3.580  -1.505  HN3     UD4  66  
#   #
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
UD4  C2     N3      SING  N  N   1  
UD4  C4     N3      SING  N  N   2  
UD4  N1     C2      SING  N  N   3  
UD4  C2     O2      DOUB  N  N   4  
UD4  C1B    N1      SING  N  N   5  
UD4  C6     N1      SING  N  N   6  
UD4  C5     C4      SING  N  N   7  
UD4  C4     O4      DOUB  N  N   8  
UD4  C6     C5      DOUB  N  N   9  
UD4  C5     H5      SING  N  N  10  
UD4  C6     H6      SING  N  N  11  
UD4  "O7'"  "C7'"   DOUB  N  N  12  
UD4  "C8'"  "C7'"   SING  N  N  13  
UD4  "C7'"  "N2'"   SING  N  N  14  
UD4  "C8'"  "H8'"   SING  N  N  15  
UD4  "C8'"  "H8'A"  SING  N  N  16  
UD4  "C8'"  "H8'B"  SING  N  N  17  
UD4  "N2'"  "C2'"   SING  N  N  18  
UD4  "N2'"  "HN2'"  SING  N  N  19  
UD4  "C2'"  "C3'"   SING  N  N  20  
UD4  "C2'"  "C1'"   SING  N  N  21  
UD4  "C2'"  "H2'"   SING  N  N  22  
UD4  "O3'"  "C3'"   SING  N  N  23  
UD4  "C3'"  "C4'"   SING  N  N  24  
UD4  "C3'"  "H3'"   SING  N  N  25  
UD4  "O3'"  "HO3'"  SING  N  N  26  
UD4  "C4'"  N4A     SING  N  N  27  
UD4  "C4'"  "C5'"   SING  N  N  28  
UD4  "C4'"  "H4'"   SING  N  N  29  
UD4  N4A    HN4A    SING  N  N  30  
UD4  N4A    HN4B    SING  N  N  31  
UD4  "O5'"  "C5'"   SING  N  N  32  
UD4  "C5'"  "C6'"   SING  N  N  33  
UD4  "C5'"  "H5'"   SING  N  N  34  
UD4  "C6'"  "H6'"   SING  N  N  35  
UD4  "C6'"  "H6'A"  SING  N  N  36  
UD4  "C6'"  "H6'B"  SING  N  N  37  
UD4  "C1'"  "O5'"   SING  N  N  38  
UD4  "C1'"  "O1'"   SING  N  N  39  
UD4  "C1'"  "H1'"   SING  N  N  40  
UD4  "O1'"  PB      SING  N  N  41  
UD4  O3A    PB      SING  N  N  42  
UD4  PB     O2B     DOUB  N  N  43  
UD4  PB     O1B     SING  N  N  44  
UD4  O1B    HO1B    SING  N  N  45  
UD4  PA     O3A     SING  N  N  46  
UD4  O1A    PA      DOUB  N  N  47  
UD4  O2A    PA      SING  N  N  48  
UD4  PA     O5B     SING  N  N  49  
UD4  O2A    HO2A    SING  N  N  50  
UD4  O5B    C5B     SING  N  N  51  
UD4  C5B    C4B     SING  N  N  52  
UD4  C5B    H5B     SING  N  N  53  
UD4  C5B    H5BA    SING  N  N  54  
UD4  C2B    C4B     SING  N  N  55  
UD4  C4B    O4B     SING  N  N  56  
UD4  C4B    H4B     SING  N  N  57  
UD4  C1B    O4B     SING  N  N  58  
UD4  C2B    O3B     SING  N  N  59  
UD4  C2B    C3B     SING  N  N  60  
UD4  C2B    H2B     SING  N  N  61  
UD4  O3B    HO3B    SING  N  N  62  
UD4  "O2'"  C3B     SING  N  N  63  
UD4  C3B    C1B     SING  N  N  64  
UD4  C3B    H3B     SING  N  N  65  
UD4  "O2'"  "HO2'"  SING  N  N  66  
UD4  C1B    H1B     SING  N  N  67  
UD4  N3     HN3     SING  N  N  68  
#   #
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
UD4  SMILES            ACDLabs               10.04  "O=P(OC1OC(C(N)C(O)C1NC(=O)C)C)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O"  
UD4  SMILES_CANONICAL  CACTVS                3.341  "C[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](NC(C)=O)[C@@H](O)[C@@H]1N"  
UD4  SMILES            CACTVS                3.341  "C[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](NC(C)=O)[CH](O)[CH]1N"  
UD4  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C)O)N"  
UD4  SMILES            "OpenEye OEToolkits"  1.5.0  "CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C)O)N"  
UD4  InChI             InChI                 1.03   "InChI=1S/C17H28N4O15P2/c1-6-10(18)13(25)11(19-7(2)22)16(33-6)35-38(30,31)36-37(28,29)32-5-8-12(24)14(26)15(34-8)21-4-3-9(23)20-17(21)27/h3-4,6,8,10-16,24-26H,5,18H2,1-2H3,(H,19,22)(H,28,29)(H,30,31)(H,20,23,27)/t6-,8-,10-,11-,12-,13+,14-,15-,16-/m1/s1"  
UD4  InChIKey          InChI                 1.03   FUUMLYWEEZBCQR-UINYWEPJSA-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
UD4  "SYSTEMATIC NAME"  ACDLabs               10.04  "(2R,3R,4S,5S,6R)-3-(acetylamino)-5-amino-4-hydroxy-6-methyltetrahydro-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)"  
UD4  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(2R,3R,4S,5S,6R)-3-acetamido-5-amino-4-hydroxy-6-methyl-oxan-2-yl] [[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-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
UD4  "Create component"   2008-05-21  RCSB  
UD4  "Modify descriptor"  2011-06-04  RCSB  
UD4  "Modify synonyms"    2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     UD4
_pdbx_chem_comp_synonyms.name        "(2R,3R,4S,5S,6R)-3-(acetylamino)-5-amino-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
