data_U5F
#

_chem_comp.id                                   U5F
_chem_comp.name                                 "5'-O-[(R)-hydroxy{[(S)-hydroxy{[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]uridine"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C9 H17 N2 O21 P5"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2019-07-22
_chem_comp.pdbx_modified_date                   2019-11-01
_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                       644.101
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    U5F
_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       6PVX
_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
U5F  "C1'"  C1   C  0  1  N  N  R  -12.789  -17.593  11.761   5.955   0.926  -0.905  "C1'"  U5F   1  
U5F  C2     C2   C  0  1  N  N  N  -14.787  -18.909  11.353   6.639   3.079  -0.007  C2     U5F   2  
U5F  C4     C3   C  0  1  N  N  N  -15.097  -21.058  12.223   7.535   3.321   2.138  C4     U5F   3  
U5F  "C4'"  C4   C  0  1  N  N  R  -10.643  -16.956  12.578   4.711  -0.951  -1.352  "C4'"  U5F   4  
U5F  C5     C5   C  0  1  N  N  N  -13.827  -20.977  12.851   7.405   1.925   2.337  C5     U5F   5  
U5F  "C5'"  C6   C  0  1  N  N  N   -9.675  -17.708  13.490   3.950  -2.114  -0.711  "C5'"  U5F   6  
U5F  C6     C7   C  0  1  N  N  N  -13.091  -19.853  12.688   6.893   1.165   1.346  C6     U5F   7  
U5F  N1     N1   N  0  1  N  N  N  -13.582  -18.815  11.933   6.510   1.751   0.171  N1     U5F   8  
U5F  N3     N2   N  0  1  N  N  N  -15.541  -20.020  11.486   7.146   3.860   0.965  N3     U5F   9  
U5F  O01    O1   O  0  1  N  N  N   -6.504  -23.159  15.332  -3.848  -1.109   2.686  O01    U5F  10  
U5F  O02    O2   O  0  1  N  N  N  -12.322  -25.510  13.827  -8.503   1.722  -1.614  O02    U5F  11  
U5F  O03    O3   O  0  1  N  N  N   -7.825  -24.848  13.995  -4.778  -2.302   0.665  O03    U5F  12  
U5F  O04    O4   O  0  1  N  N  N   -8.733  -22.815  12.715  -1.535  -3.451   1.441  O04    U5F  13  
U5F  O05    O5   O  0  1  N  N  N  -10.954  -22.155  13.684  -1.908  -3.393  -1.055  O05    U5F  14  
U5F  O06    O6   O  0  1  N  N  N  -10.262  -25.168  15.395  -6.206   1.957  -0.594  O06    U5F  15  
U5F  O1A    O7   O  0  1  N  N  N   -8.517  -19.038  15.776   1.458  -3.998  -0.622  O1A    U5F  16  
U5F  O1B    O8   O  0  1  N  N  N   -9.665  -26.377  17.542  -6.453   1.413   1.967  O1B    U5F  17  
U5F  O1G    O9   O  0  1  N  N  N  -12.387  -26.288  16.226  -6.927   3.378  -2.685  O1G    U5F  18  
U5F  O2     O10  O  0  1  N  N  N  -15.197  -17.973  10.695   6.297   3.578  -1.061  O2     U5F  19  
U5F  O2A    O11  O  0  1  N  N  N  -10.486  -20.626  15.893   1.879  -3.019   1.666  O2A    U5F  20  
U5F  O2B    O12  O  0  1  N  N  N   -8.460  -27.128  15.453  -7.049  -0.287   0.198  O2B    U5F  21  
U5F  O2G    O13  O  0  1  N  N  N   -7.964  -24.797  16.594  -4.598   0.213   0.541  O2G    U5F  22  
U5F  O3A    O14  O  0  1  N  N  N   -8.842  -20.579  13.798   0.038  -2.030   0.070  O3A    U5F  23  
U5F  O3B    O15  O  0  1  N  N  N   -9.000  -22.785  15.288  -2.463  -1.318   0.461  O3B    U5F  24  
U5F  O3G    O16  O  0  1  N  N  N  -10.965  -27.610  14.610  -8.017   3.845  -0.339  O3G    U5F  25  
U5F  O4     O17  O  0  1  N  N  N  -15.787  -22.051  12.343   7.994   4.028   3.017  O4     U5F  26  
U5F  "O4'"  O18  O  0  1  N  N  N  -11.382  -17.921  11.791   4.848   0.138  -0.414  "O4'"  U5F  27  
U5F  "O5'"  O19  O  0  1  N  N  N  -10.479  -18.593  14.268   2.583  -1.741  -0.522  "O5'"  U5F  28  
U5F  P01    P1   P  0  1  N  N  N   -7.800  -23.874  15.279  -3.940  -1.154   1.079  P01    U5F  29  
U5F  P02    P2   P  0  1  N  N  N   -9.352  -22.109  13.857  -1.468  -2.567   0.255  P02    U5F  30  
U5F  PA     P3   P  0  1  N  N  N   -9.550  -19.708  14.955   1.489  -2.725   0.131  PA     U5F  31  
U5F  PB     P4   P  0  1  N  N  N   -9.105  -25.890  16.261  -6.097   0.800   0.521  PB     U5F  32  
U5F  PG     P5   P  0  1  N  N  N  -11.494  -26.155  15.051  -7.437   2.704  -1.314  PG     U5F  33  
U5F  "C2'"  C8   C  0  1  N  N  R  -12.966  -16.862  13.115   6.997  -0.111  -1.380  "C2'"  U5F  34  
U5F  "C3'"  C9   C  0  1  N  N  S  -11.662  -16.063  13.301   6.160  -1.374  -1.681  "C3'"  U5F  35  
U5F  "O2'"  O20  O  0  1  N  N  N  -14.099  -15.999  13.145   7.655   0.348  -2.563  "O2'"  U5F  36  
U5F  "O3'"  O21  O  0  1  N  N  N  -11.743  -14.807  12.623   6.275  -1.734  -3.059  "O3'"  U5F  37  
U5F  H1     H1   H  0  1  N  N  N  -13.095  -16.977  10.902   5.634   1.553  -1.737  H1     U5F  38  
U5F  H2     H2   H  0  1  N  N  N  -10.052  -16.319  11.904   4.200  -0.615  -2.254  H2     U5F  39  
U5F  H3     H3   H  0  1  N  N  N  -13.455  -21.797  13.448   7.710   1.475   3.270  H3     U5F  40  
U5F  H4     H4   H  0  1  N  N  N   -8.949  -18.277  12.891   4.002  -2.985  -1.363  H4     U5F  41  
U5F  H5     H5   H  0  1  N  N  N   -9.139  -17.004  14.143   4.398  -2.354   0.253  H5     U5F  42  
U5F  H6     H6   H  0  1  N  N  N  -12.119  -19.772  13.151   6.786   0.098   1.481  H6     U5F  43  
U5F  H7     H7   H  0  1  N  N  N  -16.433  -20.074  11.036   7.232   4.816   0.820  H7     U5F  44  
U5F  H8     H8   H  0  1  N  N  N   -5.964  -23.427  14.598  -3.312  -0.380   3.029  H8     U5F  45  
U5F  H9     H9   H  0  1  N  N  N  -11.174  -22.624  12.888  -1.889  -2.875  -1.872  H9     U5F  46  
U5F  H10    H10  H  0  1  N  N  N   -9.525  -27.314  17.614  -5.869   2.132   2.243  H10    U5F  47  
U5F  H11    H11  H  0  1  N  N  N  -13.253  -25.965  16.005  -7.618   3.846  -3.173  H11    U5F  48  
U5F  H12    H12  H  0  1  N  N  N  -10.194  -20.560  16.794   1.918  -2.227   2.220  H12    U5F  49  
U5F  H13    H13  H  0  1  N  N  N  -11.246  -27.794  13.721  -7.371   4.524  -0.100  H13    U5F  50  
U5F  H14    H14  H  0  1  N  N  N  -13.037  -17.614  13.914   7.724  -0.310  -0.593  H14    U5F  51  
U5F  H15    H15  H  0  1  N  N  N  -11.411  -15.957  14.367   6.471  -2.200  -1.042  H15    U5F  52  
U5F  H16    H16  H  0  1  N  N  N  -14.156  -15.580  13.996   8.320  -0.265  -2.905  H16    U5F  53  
U5F  H17    H17  H  0  1  N  N  N  -12.372  -14.248  13.064   7.165  -2.008  -3.321  H17    U5F  54  
#   #
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
U5F  O2     C2     DOUB  N  N   1  
U5F  C2     N3     SING  N  N   2  
U5F  C2     N1     SING  N  N   3  
U5F  N3     C4     SING  N  N   4  
U5F  "C1'"  "O4'"  SING  N  N   5  
U5F  "C1'"  N1     SING  N  N   6  
U5F  "C1'"  "C2'"  SING  N  N   7  
U5F  "O4'"  "C4'"  SING  N  N   8  
U5F  N1     C6     SING  N  N   9  
U5F  C4     O4     DOUB  N  N  10  
U5F  C4     C5     SING  N  N  11  
U5F  "C4'"  "C3'"  SING  N  N  12  
U5F  "C4'"  "C5'"  SING  N  N  13  
U5F  "O3'"  "C3'"  SING  N  N  14  
U5F  C6     C5     DOUB  N  N  15  
U5F  O04    P02    DOUB  N  N  16  
U5F  "C2'"  "O2'"  SING  N  N  17  
U5F  "C2'"  "C3'"  SING  N  N  18  
U5F  "C5'"  "O5'"  SING  N  N  19  
U5F  O05    P02    SING  N  N  20  
U5F  O3A    P02    SING  N  N  21  
U5F  O3A    PA     SING  N  N  22  
U5F  O02    PG     DOUB  N  N  23  
U5F  P02    O3B    SING  N  N  24  
U5F  O03    P01    DOUB  N  N  25  
U5F  "O5'"  PA     SING  N  N  26  
U5F  O3G    PG     SING  N  N  27  
U5F  PA     O1A    DOUB  N  N  28  
U5F  PA     O2A    SING  N  N  29  
U5F  PG     O06    SING  N  N  30  
U5F  PG     O1G    SING  N  N  31  
U5F  P01    O3B    SING  N  N  32  
U5F  P01    O01    SING  N  N  33  
U5F  P01    O2G    SING  N  N  34  
U5F  O06    PB     SING  N  N  35  
U5F  O2B    PB     DOUB  N  N  36  
U5F  PB     O2G    SING  N  N  37  
U5F  PB     O1B    SING  N  N  38  
U5F  "C1'"  H1     SING  N  N  39  
U5F  "C4'"  H2     SING  N  N  40  
U5F  C5     H3     SING  N  N  41  
U5F  "C5'"  H4     SING  N  N  42  
U5F  "C5'"  H5     SING  N  N  43  
U5F  C6     H6     SING  N  N  44  
U5F  N3     H7     SING  N  N  45  
U5F  O01    H8     SING  N  N  46  
U5F  O05    H9     SING  N  N  47  
U5F  O1B    H10    SING  N  N  48  
U5F  O1G    H11    SING  N  N  49  
U5F  O2A    H12    SING  N  N  50  
U5F  O3G    H13    SING  N  N  51  
U5F  "C2'"  H14    SING  N  N  52  
U5F  "C3'"  H15    SING  N  N  53  
U5F  "O2'"  H16    SING  N  N  54  
U5F  "O3'"  H17    SING  N  N  55  
#   #
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
U5F  SMILES            ACDLabs               12.01  "C1(OC(C(C1O)O)COP(=O)(O)OP(=O)(O)OP(O)(=O)OP(OP(=O)(O)O)(O)=O)N2C(NC(=O)C=C2)=O"  
U5F  InChI             InChI                 1.03   "InChI=1S/C9H17N2O21P5/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(28-8)3-27-34(19,20)30-36(23,24)32-37(25,26)31-35(21,22)29-33(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H,23,24)(H,25,26)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1"  
U5F  InChIKey          InChI                 1.03   SPOOSPLWWBIUFN-XVFCMESISA-N  
U5F  SMILES_CANONICAL  CACTVS                3.385  "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"  
U5F  SMILES            CACTVS                3.385  "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"  
U5F  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O"  
U5F  SMILES            "OpenEye OEToolkits"  2.0.7  "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=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
U5F  "SYSTEMATIC NAME"  ACDLabs               12.01  "5'-O-[(R)-hydroxy{[(S)-hydroxy{[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]uridine"  
U5F  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-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
U5F  "Create component"  2019-07-22  RCSB  
U5F  "Initial release"   2019-11-06  RCSB  
##
