data_UDX
#

_chem_comp.id                                   UDX
_chem_comp.name                                 "URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C14 H22 N2 O16 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        UDP-ALPHA-D-XYLOPYRANOSE
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    1999-12-13
_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                       536.276
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    UDX
_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       1DLI
_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
UDX  "C1'"   "C1'"   C  0  1  N  N  R  -16.704  14.729  55.547  -0.186  -0.590   5.370  "C1'"   UDX   1  
UDX  "C2'"   "C2'"   C  0  1  N  N  R  -17.756  14.850  54.469  -0.246   0.226   6.663  "C2'"   UDX   2  
UDX  "O2'"   "O2'"   O  0  1  N  N  N  -17.668  16.155  53.934  -1.366   1.113   6.616  "O2'"   UDX   3  
UDX  "C3'"   "C3'"   C  0  1  N  N  S  -19.160  14.623  55.062   1.047   1.037   6.804  "C3'"   UDX   4  
UDX  "O3'"   "O3'"   O  0  1  N  N  N  -20.147  14.667  54.040   1.068   1.689   8.075  "O3'"   UDX   5  
UDX  "C4'"   "C4'"   C  0  1  N  N  R  -19.182  13.257  55.697   2.239   0.081   6.688  "C4'"   UDX   6  
UDX  "O4'"   "O4'"   O  0  1  N  N  N  -20.488  12.974  56.189   3.454   0.832   6.665  "O4'"   UDX   7  
UDX  "C5'"   "C5'"   C  0  1  N  N  N  -18.150  13.244  56.818   2.111  -0.725   5.394  "C5'"   UDX   8  
UDX  "O5'"   "O5'"   O  0  1  N  N  N  -16.842  13.506  56.269   0.912  -1.497   5.423  "O5'"   UDX   9  
UDX  PB      PB      P  0  1  N  N  S  -15.543  16.266  57.292  -0.739  -0.407   2.999  PB      UDX  10  
UDX  O1B     O1B     O  0  1  N  N  N  -14.624  15.114  57.402  -2.174  -0.611   3.299  O1B     UDX  11  
UDX  O2B     O2B     O  0  1  N  N  N  -16.106  16.883  58.529  -0.044  -1.830   2.707  O2B     UDX  12  
UDX  O3B     O3B     O  0  1  N  N  N  -16.769  15.850  56.371  -0.021   0.292   4.259  O3B     UDX  13  
UDX  O3A     O3A     O  0  1  N  N  N  -14.807  17.451  56.530  -0.591   0.537   1.704  O3A     UDX  14  
UDX  PA      PA      P  0  1  N  N  R  -14.523  17.870  55.021  -1.327  -0.219   0.488  PA      UDX  15  
UDX  O1A     O1A     O  0  1  N  N  N  -14.778  19.330  54.983  -2.752  -0.426   0.827  O1A     UDX  16  
UDX  O2A     O2A     O  0  1  N  N  N  -15.264  16.969  54.124  -0.622  -1.645   0.239  O2A     UDX  17  
UDX  O5D     O5*     O  0  1  N  N  N  -12.954  17.628  54.826  -1.217   0.674  -0.845  O5D     UDX  18  
UDX  C5D     C5*     C  0  1  N  N  N  -12.403  16.317  54.909  -1.885  -0.046  -1.882  C5D     UDX  19  
UDX  C4D     C4*     C  0  1  N  N  R  -10.889  16.375  54.817  -1.816   0.752  -3.185  C4D     UDX  20  
UDX  O4D     O4*     O  0  1  N  N  N  -10.505  16.734  53.457  -0.446   0.925  -3.581  O4D     UDX  21  
UDX  C3D     C3*     C  0  1  N  N  S  -10.336  17.459  55.732  -2.528  -0.020  -4.312  C3D     UDX  22  
UDX  O3D     O3*     O  0  1  N  N  N   -9.053  17.031  56.212  -3.617   0.739  -4.839  O3D     UDX  23  
UDX  C2D     C2*     C  0  1  N  N  R  -10.174  18.654  54.803  -1.428  -0.213  -5.389  C2D     UDX  24  
UDX  O2D     O2*     O  0  1  N  N  N   -9.117  19.488  55.229  -1.959  -0.012  -6.700  O2D     UDX  25  
UDX  C1D     C1*     C  0  1  N  N  R   -9.773  17.985  53.505  -0.418   0.904  -5.024  C1D     UDX  26  
UDX  N1      N1      N  0  1  N  N  N  -10.084  18.893  52.413   0.923   0.569  -5.509  N1      UDX  27  
UDX  C6      C6      C  0  1  N  N  N  -11.380  19.132  52.068   1.584   1.443  -6.329  C6      UDX  28  
UDX  C2      C2      C  0  1  N  N  N   -9.048  19.467  51.754   1.495  -0.590  -5.140  C2      UDX  29  
UDX  O2      O2      O  0  1  N  N  N   -7.880  19.268  52.071   0.889  -1.352  -4.411  O2      UDX  30  
UDX  N3      N3      N  0  1  N  N  N   -9.418  20.295  50.715   2.724  -0.924  -5.575  N3      UDX  31  
UDX  C4      C4      C  0  1  N  N  N  -10.709  20.581  50.316   3.409  -0.091  -6.384  C4      UDX  32  
UDX  O4      O4      O  0  1  N  N  N  -10.931  21.356  49.395   4.523  -0.390  -6.774  O4      UDX  33  
UDX  C5      C5      C  0  1  N  N  N  -11.711  19.933  51.076   2.820   1.135  -6.776  C5      UDX  34  
UDX  "H1'"   "H1'"   H  0  1  N  N  N  -15.690  14.695  55.083  -1.114  -1.151   5.253  "H1'"   UDX  35  
UDX  "H2'1"  "1H2'"  H  0  0  N  N  N  -17.587  14.083  53.676  -0.348  -0.445   7.515  "H2'1"  UDX  36  
UDX  "HO'2"  "2HO'"  H  0  0  N  N  N  -18.329  16.231  53.256  -2.155   0.562   6.522  "HO'2"  UDX  37  
UDX  "H3'1"  "1H3'"  H  0  0  N  N  N  -19.381  15.420  55.809   1.100   1.782   6.010  "H3'1"  UDX  38  
UDX  "HO'3"  "3HO'"  H  0  0  N  N  N  -21.012  14.527  54.405   1.897   2.185   8.121  "HO'3"  UDX  39  
UDX  "H4'1"  "1H4'"  H  0  0  N  N  N  -18.927  12.467  54.952   2.246  -0.597   7.542  "H4'1"  UDX  40  
UDX  "HO'4"  "4HO'"  H  0  0  N  N  N  -20.501  12.112  56.589   4.177   0.194   6.589  "HO'4"  UDX  41  
UDX  "H5'1"  "1H5'"  H  0  0  N  N  N  -18.411  13.950  57.640   2.082  -0.043   4.544  "H5'1"  UDX  42  
UDX  "H5'2"  "2H5'"  H  0  0  N  N  N  -18.178  12.297  57.406   2.968  -1.390   5.295  "H5'2"  UDX  43  
UDX  HOB2    2HOB    H  0  0  N  N  N  -16.696  17.623  58.458   0.886  -1.652   2.516  HOB2    UDX  44  
UDX  HOA2    2HOA    H  0  0  N  N  N  -15.094  17.219  53.223   0.302  -1.465   0.021  HOA2    UDX  45  
UDX  H5A1    1H5*    H  0  0  N  N  N  -12.743  15.780  55.824  -1.400  -1.012  -2.023  H5A1    UDX  46  
UDX  H5A2    2H5*    H  0  0  N  N  N  -12.840  15.633  54.144  -2.928  -0.199  -1.604  H5A2    UDX  47  
UDX  H4A1    1H4*    H  0  0  N  N  N  -10.486  15.377  55.111  -2.288   1.725  -3.048  H4A1    UDX  48  
UDX  H3A1    1H3*    H  0  0  N  N  N  -10.977  17.685  56.615  -2.879  -0.986  -3.948  H3A1    UDX  49  
UDX  HOA3    3HO*    H  0  0  N  N  N   -8.707  17.707  56.782  -3.981   0.231  -5.577  HOA3    UDX  50  
UDX  H2A1    1H2*    H  0  0  N  N  N  -11.085  19.293  54.747  -0.967  -1.197  -5.304  H2A1    UDX  51  
UDX  HOC2    2HO*    H  0  0  N  N  N   -9.015  20.233  54.649  -2.577  -0.737  -6.865  HOC2    UDX  52  
UDX  "H1'1"  1H1*    H  0  0  N  N  N   -8.684  17.759  53.424  -0.743   1.862  -5.429  "H1'1"  UDX  53  
UDX  H61     1H6     H  0  1  N  N  N  -12.204  18.651  52.620   1.119   2.374  -6.618  H61     UDX  54  
UDX  HN3     HN3     H  0  1  N  N  N   -8.663  20.738  50.190   3.120  -1.767  -5.302  HN3     UDX  55  
UDX  H51     1H5     H  0  1  N  N  N  -12.790  20.056  50.888   3.353   1.815  -7.424  H51     UDX  56  
#   #
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
UDX  "C1'"  "C2'"   SING  N  N   1  
UDX  "C1'"  "O5'"   SING  N  N   2  
UDX  "C1'"  O3B     SING  N  N   3  
UDX  "C1'"  "H1'"   SING  N  N   4  
UDX  "C2'"  "O2'"   SING  N  N   5  
UDX  "C2'"  "C3'"   SING  N  N   6  
UDX  "C2'"  "H2'1"  SING  N  N   7  
UDX  "O2'"  "HO'2"  SING  N  N   8  
UDX  "C3'"  "O3'"   SING  N  N   9  
UDX  "C3'"  "C4'"   SING  N  N  10  
UDX  "C3'"  "H3'1"  SING  N  N  11  
UDX  "O3'"  "HO'3"  SING  N  N  12  
UDX  "C4'"  "O4'"   SING  N  N  13  
UDX  "C4'"  "C5'"   SING  N  N  14  
UDX  "C4'"  "H4'1"  SING  N  N  15  
UDX  "O4'"  "HO'4"  SING  N  N  16  
UDX  "C5'"  "O5'"   SING  N  N  17  
UDX  "C5'"  "H5'1"  SING  N  N  18  
UDX  "C5'"  "H5'2"  SING  N  N  19  
UDX  PB     O1B     DOUB  N  N  20  
UDX  PB     O2B     SING  N  N  21  
UDX  PB     O3B     SING  N  N  22  
UDX  PB     O3A     SING  N  N  23  
UDX  O2B    HOB2    SING  N  N  24  
UDX  O3A    PA      SING  N  N  25  
UDX  PA     O1A     DOUB  N  N  26  
UDX  PA     O2A     SING  N  N  27  
UDX  PA     O5D     SING  N  N  28  
UDX  O2A    HOA2    SING  N  N  29  
UDX  O5D    C5D     SING  N  N  30  
UDX  C5D    C4D     SING  N  N  31  
UDX  C5D    H5A1    SING  N  N  32  
UDX  C5D    H5A2    SING  N  N  33  
UDX  C4D    O4D     SING  N  N  34  
UDX  C4D    C3D     SING  N  N  35  
UDX  C4D    H4A1    SING  N  N  36  
UDX  O4D    C1D     SING  N  N  37  
UDX  C3D    O3D     SING  N  N  38  
UDX  C3D    C2D     SING  N  N  39  
UDX  C3D    H3A1    SING  N  N  40  
UDX  O3D    HOA3    SING  N  N  41  
UDX  C2D    O2D     SING  N  N  42  
UDX  C2D    C1D     SING  N  N  43  
UDX  C2D    H2A1    SING  N  N  44  
UDX  O2D    HOC2    SING  N  N  45  
UDX  C1D    N1      SING  N  N  46  
UDX  C1D    "H1'1"  SING  N  N  47  
UDX  N1     C6      SING  N  N  48  
UDX  N1     C2      SING  N  N  49  
UDX  C6     C5      DOUB  N  N  50  
UDX  C6     H61     SING  N  N  51  
UDX  C2     O2      DOUB  N  N  52  
UDX  C2     N3      SING  N  N  53  
UDX  N3     C4      SING  N  N  54  
UDX  N3     HN3     SING  N  N  55  
UDX  C4     O4      DOUB  N  N  56  
UDX  C4     C5      SING  N  N  57  
UDX  C5     H51     SING  N  N  58  
#   #
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
UDX  SMILES            ACDLabs               10.04  "O=P(OC1OCC(O)C(O)C1O)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O"  
UDX  SMILES_CANONICAL  CACTVS                3.341  "O[C@@H]1CO[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]1O"  
UDX  SMILES            CACTVS                3.341  "O[CH]1CO[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]1O"  
UDX  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C1[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)O)O)O"  
UDX  SMILES            "OpenEye OEToolkits"  1.5.0  "C1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)O)O)O"  
UDX  InChI             InChI                 1.03   "InChI=1S/C14H22N2O16P2/c17-5-3-28-13(11(22)8(5)19)31-34(26,27)32-33(24,25)29-4-6-9(20)10(21)12(30-6)16-2-1-7(18)15-14(16)23/h1-2,5-6,8-13,17,19-22H,3-4H2,(H,24,25)(H,26,27)(H,15,18,23)/t5-,6-,8+,9-,10-,11-,12-,13-/m1/s1"  
UDX  InChIKey          InChI                 1.03   DQQDLYVHOTZLOR-OCIMBMBZSA-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
UDX  "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)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)"  
UDX  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] [(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-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
UDX  "Create component"   1999-12-13  RCSB  
UDX  "Modify descriptor"  2011-06-04  RCSB  
UDX  "Modify synonyms"    2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     UDX
_pdbx_chem_comp_synonyms.name        UDP-ALPHA-D-XYLOPYRANOSE
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
