data_1YF
#

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

_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C17 H27 N3 O15 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2013-08-05
_chem_comp.pdbx_modified_date                   2013-08-21
_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                       575.355
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    1YF
_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       4LY3
_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
1YF  O1F    O1F    O  0  1  N  N  N   -1.141  11.591  49.726   4.414  -2.272  -3.209  O1F    1YF   1  
1YF  C1F    C1F    C  0  1  N  N  N   -2.218  11.621  50.449   5.341  -2.976  -2.869  C1F    1YF   2  
1YF  N3Q    N3Q    N  0  1  N  N  N   -2.906  12.764  51.085   5.817  -2.903  -1.610  N3Q    1YF   3  
1YF  C3Q    C3Q    C  0  1  N  N  S   -4.258  12.764  51.696   5.214  -1.972  -0.653  C3Q    1YF   4  
1YF  C2Q    C2Q    C  0  1  N  N  R   -5.335  13.237  50.709   5.856  -0.590  -0.808  C2Q    1YF   5  
1YF  O2Q    O2Q    O  0  1  N  N  N   -5.400  12.240  49.667   5.576  -0.077  -2.112  O2Q    1YF   6  
1YF  C4Q    C4Q    C  0  1  N  N  S   -4.289  13.683  52.907   5.454  -2.477   0.773  C4Q    1YF   7  
1YF  O4Q    O4Q    O  0  1  N  N  N   -3.350  13.127  53.836   4.798  -3.734   0.952  O4Q    1YF   8  
1YF  C5Q    C5Q    C  0  1  N  N  R   -5.673  13.816  53.536   4.891  -1.459   1.768  C5Q    1YF   9  
1YF  C6Q    C6Q    C  0  1  N  N  N   -5.621  14.760  54.736   5.180  -1.928   3.196  C6Q    1YF  10  
1YF  O5Q    O5Q    O  0  1  N  N  N   -6.647  14.272  52.582   5.507  -0.189   1.549  O5Q    1YF  11  
1YF  C1Q    C1Q    C  0  1  N  N  R   -6.679  13.484  51.387   5.277   0.355   0.248  C1Q    1YF  12  
1YF  O3B    O3B    O  0  1  N  N  N   -7.272  12.208  51.692   3.872   0.503   0.036  O3B    1YF  13  
1YF  PB     PB     P  0  1  N  N  N   -8.887  12.119  51.827   3.064   1.843   0.416  PB     1YF  14  
1YF  O2B    O2B    O  0  1  N  N  N   -9.524  13.251  51.082   3.292   2.168   1.842  O2B    1YF  15  
1YF  O1B    O1B    O  0  1  N  N  N   -9.068  10.662  51.426   3.581   3.060  -0.502  O1B    1YF  16  
1YF  O3A    O3A    O  0  1  N  N  N   -8.869  12.371  53.411   1.491   1.611   0.164  O3A    1YF  17  
1YF  PA     PA     P  0  1  N  N  N   -9.859  12.254  54.660   0.159   2.396   0.612  PA     1YF  18  
1YF  O1A    O1A    O  0  1  N  N  N  -10.431  13.631  54.903   0.352   3.850   0.413  O1A    1YF  19  
1YF  O2A    O2A    O  0  1  N  N  N   -9.068  11.652  55.788  -0.140   2.102   2.167  O2A    1YF  20  
1YF  "O5'"  "O5'"  O  0  1  N  N  N  -11.063  11.360  54.161  -1.086   1.893  -0.278  "O5'"  1YF  21  
1YF  "C5'"  "C5'"  C  0  1  N  N  N  -10.874   9.955  54.122  -2.388   2.474  -0.192  "C5'"  1YF  22  
1YF  "C4'"  "C4'"  C  0  1  N  N  R  -12.041   9.384  53.326  -3.328   1.764  -1.169  "C4'"  1YF  23  
1YF  "O4'"  "O4'"  O  0  1  N  N  N  -13.236   9.765  53.976  -3.540   0.394  -0.765  "O4'"  1YF  24  
1YF  "C3'"  "C3'"  C  0  1  N  N  S  -12.193   9.944  51.922  -4.748   2.382  -1.107  "C3'"  1YF  25  
1YF  "O3'"  "O3'"  O  0  1  N  N  N  -11.332   9.315  50.985  -4.852   3.509  -1.980  "O3'"  1YF  26  
1YF  "C2'"  "C2'"  C  0  1  N  N  N  -13.656   9.628  51.688  -5.633   1.213  -1.605  "C2'"  1YF  27  
1YF  "C1'"  "C1'"  C  0  1  N  N  R  -14.273   9.872  53.045  -4.766  -0.040  -1.378  "C1'"  1YF  28  
1YF  N1     N1     N  0  1  N  N  N  -14.899  11.173  53.262  -5.463  -0.975  -0.491  N1     1YF  29  
1YF  C2     C2     C  0  1  N  N  N  -16.205  11.291  52.951  -5.717  -0.622   0.782  C2     1YF  30  
1YF  O2     O2     O  0  1  N  N  N  -16.945  10.265  52.399  -5.364   0.471   1.183  O2     1YF  31  
1YF  C6     C6     C  0  1  N  N  N  -14.208  12.171  53.847  -5.855  -2.196  -0.967  C6     1YF  32  
1YF  C5     C5     C  0  1  N  N  N  -14.811  13.413  54.043  -6.498  -3.057  -0.150  C5     1YF  33  
1YF  C5M    C5M    C  0  1  N  N  N  -14.088  14.603  54.666  -6.937  -4.407  -0.656  C5M    1YF  34  
1YF  C4     C4     C  0  1  N  N  N  -16.158  13.518  53.736  -6.754  -2.675   1.189  C4     1YF  35  
1YF  N3     N3     N  0  1  N  N  N  -16.814  12.481  53.172  -6.356  -1.461   1.618  N3     1YF  36  
1YF  O4     O4     O  0  1  N  N  N  -16.828  14.680  53.963  -7.333  -3.435   1.945  O4     1YF  37  
1YF  H2     H2     H  0  1  N  N  N   -2.685  10.661  50.611   5.782  -3.665  -3.574  H2     1YF  38  
1YF  H3     H3     H  0  1  N  N  N   -4.507  11.743  52.022   4.142  -1.901  -0.839  H3     1YF  39  
1YF  H4     H4     H  0  1  N  N  N   -4.996  14.188  50.273   6.935  -0.672  -0.671  H4     1YF  40  
1YF  H5     H5     H  0  1  N  N  N   -4.539  12.128  49.281   5.950   0.799  -2.279  H5     1YF  41  
1YF  H6     H6     H  0  1  N  N  N   -3.952  14.682  52.595   6.524  -2.597   0.942  H6     1YF  42  
1YF  H7     H7     H  0  1  N  N  N   -3.325  13.663  54.620   4.908  -4.113   1.834  H7     1YF  43  
1YF  H8     H8     H  0  1  N  N  N   -5.972  12.823  53.903   3.814  -1.370   1.626  H8     1YF  44  
1YF  H9     H9     H  0  1  N  N  N   -4.872  14.398  55.456   6.257  -2.017   3.338  H9     1YF  45  
1YF  H10    H10    H  0  1  N  N  N   -5.345  15.769  54.397   4.778  -1.203   3.904  H10    1YF  46  
1YF  H11    H11    H  0  1  N  N  N   -6.608  14.793  55.220   4.710  -2.897   3.362  H11    1YF  47  
1YF  H12    H12    H  0  1  N  N  N   -7.322  13.994  50.655   5.761   1.328   0.170  H12    1YF  48  
1YF  H13    H13    H  0  1  N  N  N   -9.628  10.611  50.660   3.463   2.915  -1.450  H13    1YF  49  
1YF  H14    H14    H  0  1  N  N  N   -9.046  12.258  56.519  -0.278   1.166   2.371  H14    1YF  50  
1YF  H15    H15    H  0  1  N  N  N  -10.872   9.543  55.142  -2.769   2.365   0.823  H15    1YF  51  
1YF  H16    H16    H  0  1  N  N  N   -9.922   9.713  53.627  -2.332   3.532  -0.447  H16    1YF  52  
1YF  H17    H17    H  0  1  N  N  N  -11.950   8.289  53.277  -2.931   1.808  -2.183  H17    1YF  53  
1YF  H18    H18    H  0  1  N  N  N  -12.042  11.034  51.936  -5.008   2.659  -0.085  H18    1YF  54  
1YF  H19    H19    H  0  1  N  N  N  -10.431   9.546  51.177  -5.722   3.930  -1.977  H19    1YF  55  
1YF  H20    H20    H  0  1  N  N  N  -14.089  10.297  50.930  -6.550   1.153  -1.019  H20    1YF  56  
1YF  H21    H21    H  0  1  N  N  N  -13.790   8.582  51.374  -5.862   1.332  -2.664  H21    1YF  57  
1YF  H22    H22    H  0  1  N  N  N  -15.019   9.085  53.229  -4.555  -0.522  -2.333  H22    1YF  58  
1YF  H23    H23    H  0  1  N  N  N  -13.188  12.009  54.164  -5.651  -2.470  -1.992  H23    1YF  59  
1YF  H24    H24    H  0  1  N  N  N  -13.034  14.342  54.840  -6.141  -5.134  -0.491  H24    1YF  60  
1YF  H25    H25    H  0  1  N  N  N  -14.144  15.464  53.984  -7.833  -4.722  -0.121  H25    1YF  61  
1YF  H26    H26    H  0  1  N  N  N  -14.565  14.862  55.623  -7.154  -4.342  -1.722  H26    1YF  62  
1YF  H27    H27    H  0  1  N  N  N  -17.773  12.594  52.911  -6.531  -1.190   2.533  H27    1YF  63  
1YF  H1     H1     H  0  1  N  N  N   -2.407  13.630  51.106   6.558  -3.466  -1.338  H1     1YF  64  
#   #
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
1YF  O2Q    C2Q    SING  N  N   1  
1YF  O1F    C1F    DOUB  N  N   2  
1YF  C1F    N3Q    SING  N  N   3  
1YF  C2Q    C1Q    SING  N  N   4  
1YF  C2Q    C3Q    SING  N  N   5  
1YF  "O3'"  "C3'"  SING  N  N   6  
1YF  O2B    PB     DOUB  N  N   7  
1YF  N3Q    C3Q    SING  N  N   8  
1YF  C1Q    O3B    SING  N  N   9  
1YF  C1Q    O5Q    SING  N  N  10  
1YF  O1B    PB     SING  N  N  11  
1YF  "C2'"  "C3'"  SING  N  N  12  
1YF  "C2'"  "C1'"  SING  N  N  13  
1YF  O3B    PB     SING  N  N  14  
1YF  C3Q    C4Q    SING  N  N  15  
1YF  PB     O3A    SING  N  N  16  
1YF  "C3'"  "C4'"  SING  N  N  17  
1YF  O2     C2     DOUB  N  N  18  
1YF  O5Q    C5Q    SING  N  N  19  
1YF  C4Q    C5Q    SING  N  N  20  
1YF  C4Q    O4Q    SING  N  N  21  
1YF  C2     N3     SING  N  N  22  
1YF  C2     N1     SING  N  N  23  
1YF  "C1'"  N1     SING  N  N  24  
1YF  "C1'"  "O4'"  SING  N  N  25  
1YF  N3     C4     SING  N  N  26  
1YF  N1     C6     SING  N  N  27  
1YF  "C4'"  "O4'"  SING  N  N  28  
1YF  "C4'"  "C5'"  SING  N  N  29  
1YF  O3A    PA     SING  N  N  30  
1YF  C5Q    C6Q    SING  N  N  31  
1YF  C4     O4     DOUB  N  N  32  
1YF  C4     C5     SING  N  N  33  
1YF  C6     C5     DOUB  N  N  34  
1YF  C5     C5M    SING  N  N  35  
1YF  "C5'"  "O5'"  SING  N  N  36  
1YF  "O5'"  PA     SING  N  N  37  
1YF  PA     O1A    DOUB  N  N  38  
1YF  PA     O2A    SING  N  N  39  
1YF  C1F    H2     SING  N  N  40  
1YF  C3Q    H3     SING  N  N  41  
1YF  C2Q    H4     SING  N  N  42  
1YF  O2Q    H5     SING  N  N  43  
1YF  C4Q    H6     SING  N  N  44  
1YF  O4Q    H7     SING  N  N  45  
1YF  C5Q    H8     SING  N  N  46  
1YF  C6Q    H9     SING  N  N  47  
1YF  C6Q    H10    SING  N  N  48  
1YF  C6Q    H11    SING  N  N  49  
1YF  C1Q    H12    SING  N  N  50  
1YF  O1B    H13    SING  N  N  51  
1YF  O2A    H14    SING  N  N  52  
1YF  "C5'"  H15    SING  N  N  53  
1YF  "C5'"  H16    SING  N  N  54  
1YF  "C4'"  H17    SING  N  N  55  
1YF  "C3'"  H18    SING  N  N  56  
1YF  "O3'"  H19    SING  N  N  57  
1YF  "C2'"  H20    SING  N  N  58  
1YF  "C2'"  H21    SING  N  N  59  
1YF  "C1'"  H22    SING  N  N  60  
1YF  C6     H23    SING  N  N  61  
1YF  C5M    H24    SING  N  N  62  
1YF  C5M    H25    SING  N  N  63  
1YF  C5M    H26    SING  N  N  64  
1YF  N3     H27    SING  N  N  65  
1YF  N3Q    H1     SING  N  N  66  
#   #
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
1YF  SMILES            ACDLabs               12.01  "O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(O)C(NC=O)C3O)C)O)O)C"  
1YF  InChI             InChI                 1.03   "InChI=1S/C17H27N3O15P2/c1-7-4-20(17(26)19-15(7)25)11-3-9(22)10(33-11)5-31-36(27,28)35-37(29,30)34-16-14(24)12(18-6-21)13(23)8(2)32-16/h4,6,8-14,16,22-24H,3,5H2,1-2H3,(H,18,21)(H,27,28)(H,29,30)(H,19,25,26)/t8-,9+,10-,11-,12+,13-,14-,16-/m1/s1"  
1YF  InChIKey          InChI                 1.03   XDTNOGIJZRWAPO-ADAYKIPUSA-N  
1YF  SMILES_CANONICAL  CACTVS                3.385  "C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@@H](NC=O)[C@@H]1O"  
1YF  SMILES            CACTVS                3.385  "C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](NC=O)[CH]1O"  
1YF  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)NC=O)O"  
1YF  SMILES            "OpenEye OEToolkits"  1.7.6  "CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)NC=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
1YF  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2R,3R,4S,5S,6R)-4-(formylamino)-3,5-dihydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)"  
1YF  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "[(2R,3R,4S,5S,6R)-4-formamido-6-methyl-3,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-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
1YF  "Create component"    2013-08-05  RCSB  
1YF  "Initial release"     2013-08-14  RCSB  
1YF  "Other modification"  2013-08-16  RCSB  
1YF  "Modify name"         2013-08-21  RCSB  
##
