data_3YN
#

_chem_comp.id                                   3YN
_chem_comp.name                                 
;[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl
(2R,4R,6R)-4-hydroxy-6-methyl-5-oxotetrahydro-2H-pyran-2-yl dihydrogen diphosphate
;

_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C16 H24 N2 O14 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        TDP-4-keto-D-olivose
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2014-12-10
_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                       530.314
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    3YN
_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       4RVH
_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
3YN  O4P    O4P    O  0  1  N  N  N  -22.952   4.353  14.350  -3.814  -2.328  -0.529  O4P    3YN   1  
3YN  P2     P2     P  0  1  N  N  N  -22.968   4.729  12.940  -3.227  -1.019   0.202  P2     3YN   2  
3YN  O3P    O3P    O  0  1  N  N  N  -22.790   6.146  12.594  -3.563  -1.067   1.643  O3P    3YN   3  
3YN  O1     O1     O  0  1  N  N  N  -24.348   4.242  12.387  -3.875   0.300  -0.456  O1     3YN   4  
3YN  C1     C1     C  0  1  N  N  R  -24.595   4.048  11.010  -5.268   0.608  -0.371  C1     3YN   5  
3YN  C2     C2     C  0  1  N  N  N  -26.038   4.410  10.732  -5.691   1.397  -1.613  C2     3YN   6  
3YN  C3     C3     C  0  1  N  N  R  -26.990   3.466  11.455  -7.194   1.691  -1.531  C3     3YN   7  
3YN  O3     O3     O  0  1  N  N  N  -28.320   3.663  11.024  -7.933   0.474  -1.653  O3     3YN   8  
3YN  C4     C4     C  0  1  N  N  N  -26.608   2.045  11.221  -7.473   2.327  -0.184  C4     3YN   9  
3YN  O4     O4     O  0  1  N  N  N  -27.431   1.203  11.025  -8.134   3.333  -0.094  O4     3YN  10  
3YN  C5     C5     C  0  1  N  N  R  -25.152   1.744  11.327  -6.896   1.657   1.045  C5     3YN  11  
3YN  O5     O5     O  0  1  N  N  N  -24.413   2.694  10.605  -5.511   1.386   0.801  O5     3YN  12  
3YN  C6     C6     C  0  1  N  N  N  -24.862   0.381  10.780  -7.640   0.348   1.316  C6     3YN  13  
3YN  OPP    OPP    O  0  1  N  N  N  -22.002   3.800  12.106  -1.628  -0.977   0.025  OPP    3YN  14  
3YN  P      P      P  0  1  N  N  N  -20.454   3.536  12.198  -0.407  -1.786   0.693  P      3YN  15  
3YN  O1P    O1P    O  0  1  N  N  N  -20.118   2.997  10.900  -0.734  -3.229   0.731  O1P    3YN  16  
3YN  O2P    O2P    O  0  1  N  N  N  -20.178   2.705  13.341  -0.164  -1.251   2.192  O2P    3YN  17  
3YN  "O5'"  "O5'"  O  0  1  N  N  N  -19.742   4.912  12.406   0.928  -1.561  -0.179  "O5'"  3YN  18  
3YN  "C5'"  "C5'"  C  0  1  N  N  N  -18.358   4.991  12.643   2.159  -2.232   0.095  "C5'"  3YN  19  
3YN  "C4'"  "C4'"  C  0  1  N  N  R  -17.895   6.423  12.589   3.217  -1.791  -0.919  "C4'"  3YN  20  
3YN  "O4'"  "O4'"  O  0  1  N  N  N  -16.564   6.448  13.052   3.543  -0.396  -0.740  "O4'"  3YN  21  
3YN  "C3'"  "C3'"  C  0  1  N  N  S  -17.864   6.951  11.184   4.562  -2.513  -0.653  "C3'"  3YN  22  
3YN  "O3'"  "O3'"  O  0  1  N  N  N  -18.289   8.287  11.227   4.600  -3.780  -1.313  "O3'"  3YN  23  
3YN  "C2'"  "C2'"  C  0  1  N  N  N  -16.419   6.943  10.781   5.585  -1.534  -1.278  "C2'"  3YN  24  
3YN  "C1'"  "C1'"  C  0  1  N  N  R  -15.671   6.946  12.091   4.837  -0.188  -1.330  "C1'"  3YN  25  
3YN  N11    N11    N  0  1  N  N  N  -14.442   6.182  12.067   5.575   0.822  -0.568  N11    3YN  26  
3YN  C21    C21    C  0  1  N  N  N  -13.233   6.839  12.306   5.719   0.680   0.762  C21    3YN  27  
3YN  O21    O21    O  0  1  N  N  N  -13.208   8.034  12.526   5.233  -0.287   1.318  O21    3YN  28  
3YN  N31    N31    N  0  1  N  N  N  -12.088   6.227  12.302   6.392   1.593   1.487  N31    3YN  29  
3YN  C41    C41    C  0  1  N  N  N  -12.038   4.942  12.076   6.937   2.670   0.886  C41    3YN  30  
3YN  O41    O41    O  0  1  N  N  N  -10.960   4.376  12.075   7.547   3.496   1.541  O41    3YN  31  
3YN  C51    C51    C  0  1  N  N  N  -13.268   4.202  11.830   6.793   2.832  -0.513  C51    3YN  32  
3YN  C5A    C5A    C  0  1  N  N  N  -13.180   2.743  11.563   7.398   4.023  -1.210  C5A    3YN  33  
3YN  C61    C61    C  0  1  N  N  N  -14.464   4.878  11.840   6.118   1.898  -1.217  C61    3YN  34  
3YN  H1     H1     H  0  1  N  N  N  -22.820   5.128  14.883  -3.631  -2.363  -1.478  H1     3YN  35  
3YN  H2     H2     H  0  1  N  N  N  -23.946   4.707  10.414  -5.841  -0.318  -0.317  H2     3YN  36  
3YN  H3     H3     H  0  1  N  N  N  -26.223   5.439  11.075  -5.137   2.335  -1.656  H3     3YN  37  
3YN  H4     H4     H  0  1  N  N  N  -26.222   4.346   9.649  -5.483   0.808  -2.507  H4     3YN  38  
3YN  H5     H5     H  0  1  N  N  N  -26.919   3.672  12.533  -7.480   2.377  -2.328  H5     3YN  39  
3YN  H6     H6     H  0  1  N  N  N  -28.704   2.827  10.789  -8.892   0.589  -1.610  H6     3YN  40  
3YN  H7     H7     H  0  1  N  N  N  -24.861   1.768  12.388  -6.995   2.320   1.905  H7     3YN  41  
3YN  H8     H8     H  0  1  N  N  N  -25.438  -0.370  11.341  -7.531  -0.316   0.458  H8     3YN  42  
3YN  H9     H9     H  0  1  N  N  N  -25.147   0.344   9.718  -7.222  -0.131   2.201  H9     3YN  43  
3YN  H10    H10    H  0  1  N  N  N  -23.787   0.168  10.878  -8.697   0.558   1.481  H10    3YN  44  
3YN  H11    H11    H  0  1  N  N  N  -19.796   1.885  13.052   0.055  -0.311   2.244  H11    3YN  45  
3YN  H12    H12    H  0  1  N  N  N  -18.137   4.576  13.637   2.494  -1.980   1.102  H12    3YN  46  
3YN  H13    H13    H  0  1  N  N  N  -17.826   4.409  11.876   2.011  -3.309   0.021  H13    3YN  47  
3YN  H14    H14    H  0  1  N  N  N  -18.548   7.052  13.213   2.873  -1.977  -1.936  H14    3YN  48  
3YN  H15    H15    H  0  1  N  N  N  -18.471   6.330  10.509   4.737  -2.629   0.417  H15    3YN  49  
3YN  H16    H16    H  0  1  N  N  N  -19.204   8.321  11.481   5.422  -4.271  -1.177  H16    3YN  50  
3YN  H17    H17    H  0  1  N  N  N  -16.181   6.041  10.198   6.471  -1.454  -0.649  H17    3YN  51  
3YN  H18    H18    H  0  1  N  N  N  -16.174   7.837  10.189   5.858  -1.858  -2.283  H18    3YN  52  
3YN  H19    H19    H  0  1  N  N  N  -15.427   7.991  12.334   4.725   0.134  -2.365  H19    3YN  53  
3YN  H20    H20    H  0  1  N  N  N  -11.246   6.739  12.472   6.486   1.475   2.445  H20    3YN  54  
3YN  H21    H21    H  0  1  N  N  N  -12.128   2.425  11.606   6.671   4.835  -1.237  H21    3YN  55  
3YN  H22    H22    H  0  1  N  N  N  -13.760   2.196  12.321   8.286   4.348  -0.669  H22    3YN  56  
3YN  H23    H23    H  0  1  N  N  N  -13.587   2.528  10.564   7.672   3.748  -2.228  H23    3YN  57  
3YN  H24    H24    H  0  1  N  N  N  -15.396   4.360  11.668   5.998   2.004  -2.285  H24    3YN  58  
#   #
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
3YN  O5     C1     SING  N  N   1  
3YN  O5     C5     SING  N  N   2  
3YN  C2     C1     SING  N  N   3  
3YN  C2     C3     SING  N  N   4  
3YN  C6     C5     SING  N  N   5  
3YN  "C2'"  "C3'"  SING  N  N   6  
3YN  "C2'"  "C1'"  SING  N  N   7  
3YN  O1P    P      DOUB  N  N   8  
3YN  C1     O1     SING  N  N   9  
3YN  O3     C3     SING  N  N  10  
3YN  O4     C4     DOUB  N  N  11  
3YN  "C3'"  "O3'"  SING  N  N  12  
3YN  "C3'"  "C4'"  SING  N  N  13  
3YN  C4     C5     SING  N  N  14  
3YN  C4     C3     SING  N  N  15  
3YN  C5A    C51    SING  N  N  16  
3YN  C51    C61    DOUB  N  N  17  
3YN  C51    C41    SING  N  N  18  
3YN  C61    N11    SING  N  N  19  
3YN  N11    "C1'"  SING  N  N  20  
3YN  N11    C21    SING  N  N  21  
3YN  O41    C41    DOUB  N  N  22  
3YN  C41    N31    SING  N  N  23  
3YN  "C1'"  "O4'"  SING  N  N  24  
3YN  OPP    P      SING  N  N  25  
3YN  OPP    P2     SING  N  N  26  
3YN  P      "O5'"  SING  N  N  27  
3YN  P      O2P    SING  N  N  28  
3YN  N31    C21    SING  N  N  29  
3YN  C21    O21    DOUB  N  N  30  
3YN  O1     P2     SING  N  N  31  
3YN  "O5'"  "C5'"  SING  N  N  32  
3YN  "C4'"  "C5'"  SING  N  N  33  
3YN  "C4'"  "O4'"  SING  N  N  34  
3YN  O3P    P2     DOUB  N  N  35  
3YN  P2     O4P    SING  N  N  36  
3YN  O4P    H1     SING  N  N  37  
3YN  C1     H2     SING  N  N  38  
3YN  C2     H3     SING  N  N  39  
3YN  C2     H4     SING  N  N  40  
3YN  C3     H5     SING  N  N  41  
3YN  O3     H6     SING  N  N  42  
3YN  C5     H7     SING  N  N  43  
3YN  C6     H8     SING  N  N  44  
3YN  C6     H9     SING  N  N  45  
3YN  C6     H10    SING  N  N  46  
3YN  O2P    H11    SING  N  N  47  
3YN  "C5'"  H12    SING  N  N  48  
3YN  "C5'"  H13    SING  N  N  49  
3YN  "C4'"  H14    SING  N  N  50  
3YN  "C3'"  H15    SING  N  N  51  
3YN  "O3'"  H16    SING  N  N  52  
3YN  "C2'"  H17    SING  N  N  53  
3YN  "C2'"  H18    SING  N  N  54  
3YN  "C1'"  H19    SING  N  N  55  
3YN  N31    H20    SING  N  N  56  
3YN  C5A    H21    SING  N  N  57  
3YN  C5A    H22    SING  N  N  58  
3YN  C5A    H23    SING  N  N  59  
3YN  C61    H24    SING  N  N  60  
#   #
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
3YN  SMILES            ACDLabs               12.01  "O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(=O)C(O)C3)C)O)O)C"  
3YN  InChI             InChI                 1.03   "InChI=1S/C16H24N2O14P2/c1-7-5-18(16(23)17-15(7)22)12-3-9(19)11(30-12)6-28-33(24,25)32-34(26,27)31-13-4-10(20)14(21)8(2)29-13/h5,8-13,19-20H,3-4,6H2,1-2H3,(H,24,25)(H,26,27)(H,17,22,23)/t8-,9+,10-,11-,12-,13-/m1/s1"  
3YN  InChIKey          InChI                 1.03   AONILRCSLAIOQE-LREJFELKSA-N  
3YN  SMILES_CANONICAL  CACTVS                3.385  "C[C@H]1O[C@@H](C[C@@H](O)C1=O)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"  
3YN  SMILES            CACTVS                3.385  "C[CH]1O[CH](C[CH](O)C1=O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O"  
3YN  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "C[C@@H]1C(=O)[C@@H](C[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"  
3YN  SMILES            "OpenEye OEToolkits"  1.7.6  "CC1C(=O)C(CC(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)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
3YN  "SYSTEMATIC NAME"  ACDLabs               12.01  "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,4R,6R)-4-hydroxy-6-methyl-5-oxotetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)"  
3YN  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "[[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,4R,6R)-6-methyl-4-oxidanyl-5-oxidanylidene-oxan-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
3YN  "Create component"  2014-12-10  RCSB  
3YN  "Initial release"   2015-01-28  RCSB  
3YN  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     3YN
_pdbx_chem_comp_synonyms.name        TDP-4-keto-D-olivose
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
