data_UPF
#

_chem_comp.id                                   UPF
_chem_comp.name                                 "URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUOROGALACTOSE"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C15 H23 F N2 O16 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "URIDINE-5'-MONOPHOSPHATE 2-DEOXY-2-FLUORO-GALACTOPYRANOSYL-MONOPHOSPHATE ESTER"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2000-11-30
_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                       568.293
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    UPF
_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       1GA8
_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
UPF  N1      N1      N  0  1  N  N  N  27.246  44.476  57.859   0.858  -0.674   5.805  N1      UPF   1  
UPF  C2      C2      C  0  1  N  N  N  27.632  43.844  56.664   1.590   0.372   5.383  C2      UPF   2  
UPF  N3      N3      N  0  1  N  N  N  26.736  44.095  55.610   2.870   0.523   5.772  N3      UPF   3  
UPF  C4      C4      C  0  1  N  N  N  25.543  44.905  55.653   3.444  -0.383   6.588  C4      UPF   4  
UPF  C5      C5      C  0  1  N  N  N  25.233  45.520  56.910   2.686  -1.493   7.036  C5      UPF   5  
UPF  C6      C6      C  0  1  N  N  N  26.052  45.309  57.942   1.403  -1.617   6.634  C6      UPF   6  
UPF  O2      O2      O  0  1  N  N  N  28.633  43.138  56.565   1.086   1.198   4.647  O2      UPF   7  
UPF  O4      O4      O  0  1  N  N  N  24.868  45.022  54.645   4.603  -0.250   6.936  O4      UPF   8  
UPF  C1D     C1*     C  0  1  N  N  R  27.946  44.427  59.222  -0.533  -0.809   5.369  C1D     UPF   9  
UPF  C2D     C2*     C  0  1  N  N  R  29.213  45.245  59.123  -1.346   0.460   5.726  C2D     UPF  10  
UPF  "O2'"   O2*     O  0  1  N  N  N  30.325  44.490  59.591  -1.858   0.381   7.058  "O2'"   UPF  11  
UPF  C3D     C3*     C  0  1  N  N  S  28.928  46.470  59.974  -2.497   0.412   4.687  C3D     UPF  12  
UPF  C4D     C4*     C  0  1  N  N  R  28.177  45.825  61.135  -1.951  -0.493   3.566  C4D     UPF  13  
UPF  O4D     O4*     O  0  1  N  N  N  27.357  44.776  60.451  -0.611  -0.866   3.929  O4D     UPF  14  
UPF  O3D     O3*     O  0  1  N  N  N  30.009  47.247  60.450  -3.673  -0.155   5.270  O3D     UPF  15  
UPF  C5D     C5*     C  0  1  N  N  N  26.869  46.225  61.745  -1.938   0.270   2.241  C5D     UPF  16  
UPF  O5D     O5*     O  0  1  N  N  N  26.298  47.578  61.483  -1.424  -0.574   1.209  O5D     UPF  17  
UPF  PA      PA      P  0  1  N  N  R  26.766  49.099  61.249  -1.438   0.288  -0.149  PA      UPF  18  
UPF  O1A     O1A     O  0  1  N  N  N  28.222  49.272  61.261  -2.825   0.704  -0.454  O1A     UPF  19  
UPF  O2A     O2A     O  0  1  N  N  N  26.106  49.694  60.059  -0.514   1.593   0.033  O2A     UPF  20  
UPF  O3A     O3A     O  0  1  N  N  N  26.011  49.279  62.643  -0.869  -0.607  -1.359  O3A     UPF  21  
UPF  PB      PB      P  0  1  N  N  S  25.737  50.507  63.615  -0.912   0.313  -2.680  PB      UPF  22  
UPF  O1B     O1B     O  0  1  N  N  N  27.073  51.140  63.723  -2.307   0.729  -2.946  O1B     UPF  23  
UPF  O2B     O2B     O  0  1  N  N  N  24.752  51.397  62.959   0.003   1.618  -2.454  O2B     UPF  24  
UPF  O3B     O3B     O  0  1  N  N  N  25.283  49.976  64.989  -0.352  -0.523  -3.936  O3B     UPF  25  
UPF  "C1'"   "C1'"   C  0  1  N  N  R  25.663  49.782  66.526  -0.416   0.342  -5.071  "C1'"   UPF  26  
UPF  "C2'"   "C2'"   C  0  1  N  N  R  27.142  49.349  66.499  -0.643  -0.491  -6.334  "C2'"   UPF  27  
UPF  "C3'"   "C3'"   C  0  1  N  N  S  27.570  48.162  65.500   0.503  -1.496  -6.482  "C3'"   UPF  28  
UPF  "C4'"   "C4'"   C  0  1  N  N  R  26.580  46.942  65.687   1.832  -0.733  -6.435  "C4'"   UPF  29  
UPF  "C5'"   "C5'"   C  0  1  N  N  R  25.091  47.558  65.670   1.873   0.117  -5.163  "C5'"   UPF  30  
UPF  "C6'"   "C6'"   C  0  1  N  N  N  24.067  46.500  66.124   3.210   0.856  -5.089  "C6'"   UPF  31  
UPF  "F2'"   "F2'"   F  0  1  N  N  N  28.007  50.445  66.303  -1.858  -1.177  -6.229  "F2'"   UPF  32  
UPF  "O3'"   "O3'"   O  0  1  N  N  N  28.862  47.756  65.870   0.383  -2.180  -7.731  "O3'"   UPF  33  
UPF  "O4'"   "O4'"   O  0  1  N  N  N  26.878  46.287  66.949   1.939   0.110  -7.583  "O4'"   UPF  34  
UPF  "O5'"   "O5'"   O  0  1  N  N  N  24.823  48.627  66.707   0.808   1.065  -5.184  "O5'"   UPF  35  
UPF  "O6'"   "O6'"   O  0  1  N  N  N  23.780  45.249  65.553   3.251   1.649  -3.901  "O6'"   UPF  36  
UPF  HN3     HN3     H  0  1  N  N  N  26.975  43.644  54.726   3.382   1.285   5.461  HN3     UPF  37  
UPF  H5      H5      H  0  1  N  N  N  24.354  46.163  57.085   3.129  -2.229   7.690  H5      UPF  38  
UPF  H6      H6      H  0  1  N  N  N  25.741  45.824  58.866   0.810  -2.456   6.966  H6      UPF  39  
UPF  H1D     H1*     H  0  1  N  N  N  27.995  43.318  59.331  -0.989  -1.694   5.814  H1D     UPF  40  
UPF  H2D     H2*     H  0  1  N  N  N  29.480  45.534  58.080  -0.741   1.358   5.596  H2D     UPF  41  
UPF  "HO2'"  *HO2    H  0  0  N  N  N  31.121  45.004  59.528  -2.351   1.198   7.216  "HO2'"  UPF  42  
UPF  H3D     H3*     H  0  1  N  N  N  28.405  47.242  59.363  -2.707   1.410   4.303  H3D     UPF  43  
UPF  H4D     H4*     H  0  1  N  N  N  29.017  45.834  61.868  -2.572  -1.384   3.474  H4D     UPF  44  
UPF  "HO3'"  *HO3    H  0  0  N  N  N  29.830  48.013  60.982  -3.930   0.423   6.000  "HO3'"  UPF  45  
UPF  "H5'1"  1H5*    H  0  0  N  N  N  26.104  45.462  61.466  -1.306   1.152   2.336  "H5'1"  UPF  46  
UPF  "H5'2"  2H5*    H  0  0  N  N  N  26.938  46.081  62.848  -2.953   0.576   1.987  "H5'2"  UPF  47  
UPF  HOA2    2HOA    H  0  0  N  N  N  26.382  50.592  59.920   0.378   1.278   0.230  HOA2    UPF  48  
UPF  HOB2    2HOB    H  0  0  N  N  N  24.588  52.130  63.539   0.902   1.303  -2.284  HOB2    UPF  49  
UPF  "H1'"   "H1'"   H  0  1  N  N  N  25.544  50.610  67.262  -1.241   1.043  -4.946  "H1'"   UPF  50  
UPF  "H2'"   "H2'"   H  0  1  N  N  N  27.251  48.908  67.517  -0.669   0.164  -7.204  "H2'"   UPF  51  
UPF  "H3'"   "H3'"   H  0  1  N  N  N  27.539  48.503  64.439   0.465  -2.218  -5.666  "H3'"   UPF  52  
UPF  "H4'"   "H4'"   H  0  1  N  N  N  26.681  46.177  64.881   2.659  -1.442  -6.424  "H4'"   UPF  53  
UPF  "H5'"   "H5'"   H  0  1  N  N  N  25.004  47.940  64.626   1.767  -0.528  -4.292  "H5'"   UPF  54  
UPF  "H6'1"  "1H6'"  H  0  0  N  N  N  24.310  46.290  67.191   3.317   1.502  -5.960  "H6'1"  UPF  55  
UPF  "H6'2"  "2H6'"  H  0  0  N  N  N  23.089  47.034  66.173   4.025   0.132  -5.071  "H6'2"  UPF  56  
UPF  HO3A    "'HO3"  H  0  0  N  N  N  29.114  47.055  65.280  -0.469  -2.634  -7.721  HO3A    UPF  57  
UPF  "HO4'"  "'HO4"  H  0  0  N  N  N  26.283  45.554  67.061   1.903  -0.466  -8.358  "HO4'"  UPF  58  
UPF  "HO6'"  "'HO6"  H  0  0  N  N  N  23.148  44.596  65.832   4.108   2.096  -3.893  "HO6'"  UPF  59  
#   #
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
UPF  N1     C2      SING  N  N   1  
UPF  N1     C6      SING  N  N   2  
UPF  N1     C1D     SING  N  N   3  
UPF  C2     N3      SING  N  N   4  
UPF  C2     O2      DOUB  N  N   5  
UPF  N3     C4      SING  N  N   6  
UPF  N3     HN3     SING  N  N   7  
UPF  C4     C5      SING  N  N   8  
UPF  C4     O4      DOUB  N  N   9  
UPF  C5     C6      DOUB  N  N  10  
UPF  C5     H5      SING  N  N  11  
UPF  C6     H6      SING  N  N  12  
UPF  C1D    C2D     SING  N  N  13  
UPF  C1D    O4D     SING  N  N  14  
UPF  C1D    H1D     SING  N  N  15  
UPF  C2D    "O2'"   SING  N  N  16  
UPF  C2D    C3D     SING  N  N  17  
UPF  C2D    H2D     SING  N  N  18  
UPF  "O2'"  "HO2'"  SING  N  N  19  
UPF  C3D    C4D     SING  N  N  20  
UPF  C3D    O3D     SING  N  N  21  
UPF  C3D    H3D     SING  N  N  22  
UPF  C4D    O4D     SING  N  N  23  
UPF  C4D    C5D     SING  N  N  24  
UPF  C4D    H4D     SING  N  N  25  
UPF  O3D    "HO3'"  SING  N  N  26  
UPF  C5D    O5D     SING  N  N  27  
UPF  C5D    "H5'1"  SING  N  N  28  
UPF  C5D    "H5'2"  SING  N  N  29  
UPF  O5D    PA      SING  N  N  30  
UPF  PA     O1A     DOUB  N  N  31  
UPF  PA     O2A     SING  N  N  32  
UPF  PA     O3A     SING  N  N  33  
UPF  O2A    HOA2    SING  N  N  34  
UPF  O3A    PB      SING  N  N  35  
UPF  PB     O1B     DOUB  N  N  36  
UPF  PB     O2B     SING  N  N  37  
UPF  PB     O3B     SING  N  N  38  
UPF  O2B    HOB2    SING  N  N  39  
UPF  O3B    "C1'"   SING  N  N  40  
UPF  "C1'"  "C2'"   SING  N  N  41  
UPF  "C1'"  "O5'"   SING  N  N  42  
UPF  "C1'"  "H1'"   SING  N  N  43  
UPF  "C2'"  "C3'"   SING  N  N  44  
UPF  "C2'"  "F2'"   SING  N  N  45  
UPF  "C2'"  "H2'"   SING  N  N  46  
UPF  "C3'"  "C4'"   SING  N  N  47  
UPF  "C3'"  "O3'"   SING  N  N  48  
UPF  "C3'"  "H3'"   SING  N  N  49  
UPF  "C4'"  "C5'"   SING  N  N  50  
UPF  "C4'"  "O4'"   SING  N  N  51  
UPF  "C4'"  "H4'"   SING  N  N  52  
UPF  "C5'"  "C6'"   SING  N  N  53  
UPF  "C5'"  "O5'"   SING  N  N  54  
UPF  "C5'"  "H5'"   SING  N  N  55  
UPF  "C6'"  "O6'"   SING  N  N  56  
UPF  "C6'"  "H6'1"  SING  N  N  57  
UPF  "C6'"  "H6'2"  SING  N  N  58  
UPF  "O3'"  HO3A    SING  N  N  59  
UPF  "O4'"  "HO4'"  SING  N  N  60  
UPF  "O6'"  "HO6'"  SING  N  N  61  
#   #
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
UPF  SMILES            ACDLabs               10.04  "O=P(OC1OC(C(O)C(O)C1F)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O"  
UPF  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](F)[C@@H](O)[C@H]1O"  
UPF  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](F)[CH](O)[CH]1O"  
UPF  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)F)O)O"  
UPF  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)F)O)O"  
UPF  InChI             InChI                 1.03   "InChI=1S/C15H23FN2O16P2/c16-8-11(23)9(21)5(3-19)32-14(8)33-36(28,29)34-35(26,27)30-4-6-10(22)12(24)13(31-6)18-2-1-7(20)17-15(18)25/h1-2,5-6,8-14,19,21-24H,3-4H2,(H,26,27)(H,28,29)(H,17,20,25)/t5-,6-,8-,9+,10-,11-,12-,13-,14-/m1/s1"  
UPF  InChIKey          InChI                 1.03   NGTCPFGWXMBZEP-KBQKSTHMSA-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
UPF  "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-fluoro-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)"  
UPF  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [[(2R,3R,4S,5R,6R)-3-fluoro-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-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
UPF  "Create component"   2000-11-30  RCSB  
UPF  "Modify descriptor"  2011-06-04  RCSB  
UPF  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     UPF
_pdbx_chem_comp_synonyms.name        "URIDINE-5'-MONOPHOSPHATE 2-DEOXY-2-FLUORO-GALACTOPYRANOSYL-MONOPHOSPHATE ESTER"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
