data_KYK
#

_chem_comp.id                                   KYK
_chem_comp.name                                 "N6-benzyl-(alpha,beta)-methylene-ADP"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C18 H23 N5 O9 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2019-07-05
_chem_comp.pdbx_modified_date                   2020-07-17
_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                       515.351
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    KYK
_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       6S7F
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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
KYK  N1      N1   N  0  1  Y  N  N  -13.142  23.579  -36.537  -5.229   1.737  -0.928  N1      KYK   1  
KYK  N3      N2   N  0  1  Y  N  N  -14.563  21.641  -36.616  -3.170   2.779  -1.036  N3      KYK   2  
KYK  C4      C1   C  0  1  Y  N  N  -14.478  21.647  -35.284  -2.552   1.703  -0.560  C4      KYK   3  
KYK  C5      C2   C  0  1  Y  N  N  -13.767  22.541  -34.501  -3.312   0.564  -0.244  C5      KYK   4  
KYK  C6      C3   C  0  1  Y  N  N  -13.067  23.564  -35.196  -4.701   0.616  -0.447  C6      KYK   5  
KYK  C8      C4   C  0  1  Y  N  N  -14.755  21.226  -33.159  -1.240   0.102   0.200  C8      KYK   6  
KYK  C21     C5   C  0  1  N  N  N  -12.133  24.674  -33.192  -6.948  -0.402  -0.373  C21     KYK   7  
KYK  C22     C6   C  0  1  Y  N  N   -8.962  27.479  -32.451  -8.754  -4.108   0.745  C22     KYK   8  
KYK  C24     C7   C  0  1  Y  N  N  -11.303  26.991  -32.629  -7.740  -2.714  -0.916  C24     KYK   9  
KYK  C26     C8   C  0  1  Y  N  N   -9.694  25.265  -33.016  -8.021  -1.903   1.319  C26     KYK  10  
KYK  PB      P1   P  0  1  N  N  N  -17.141  19.671  -28.920   6.823  -2.622  -0.422  PB      KYK  11  
KYK  O1B     O1   O  0  1  N  N  N  -18.317  20.536  -28.627   7.194  -3.661  -1.594  O1B     KYK  12  
KYK  O2B     O2   O  0  1  N  N  N  -16.050  19.774  -27.841   6.324  -3.433   0.877  O2B     KYK  13  
KYK  O3B     O3   O  0  1  N  N  N  -16.449  20.157  -30.208   8.018  -1.821  -0.075  O3B     KYK  14  
KYK  PA      P2   P  0  1  N  N  N  -18.977  17.712  -30.337   5.072  -0.336   0.334  PA      KYK  15  
KYK  O1A     O4   O  0  1  N  N  N  -20.272  18.455  -30.277   6.372   0.535   0.712  O1A     KYK  16  
KYK  O2A     O5   O  0  1  N  N  N  -19.202  16.175  -30.457   4.614  -1.081   1.528  O2A     KYK  17  
KYK  C3A     C9   C  0  1  N  N  N  -17.624  17.957  -29.167   5.493  -1.513  -0.993  C3A     KYK  18  
KYK  "O5'"   O6   O  0  1  N  N  N  -18.310  18.160  -31.693   3.898   0.644  -0.170  "O5'"   KYK  19  
KYK  "C5'"   C10  C  0  1  N  N  N  -17.082  17.572  -32.156   3.274   1.611   0.677  "C5'"   KYK  20  
KYK  "C4'"   C11  C  0  1  N  N  R  -16.843  17.923  -33.595   2.206   2.369  -0.115  "C4'"   KYK  21  
KYK  "O4'"   O7   O  0  1  N  N  N  -16.834  19.354  -33.764   1.133   1.478  -0.463  "O4'"   KYK  22  
KYK  "C3'"   C12  C  0  1  N  N  S  -15.483  17.467  -34.087   1.609   3.493   0.754  "C3'"   KYK  23  
KYK  "O3'"   O8   O  0  1  N  N  N  -15.556  16.078  -34.405   1.827   4.766   0.143  "O3'"   KYK  24  
KYK  "C2'"   C13  C  0  1  N  N  R  -15.218  18.423  -35.254   0.097   3.167   0.810  "C2'"   KYK  25  
KYK  "O2'"   O9   O  0  1  N  N  N  -15.802  17.964  -36.464  -0.688   4.355   0.689  "O2'"   KYK  26  
KYK  "C1'"   C14  C  0  1  N  N  R  -15.961  19.694  -34.817  -0.085   2.254  -0.435  "C1'"   KYK  27  
KYK  N9      N3   N  0  1  Y  N  N  -15.111  20.801  -34.410  -1.250   1.382  -0.270  N9      KYK  28  
KYK  N7      N4   N  0  1  Y  N  N  -13.947  22.260  -33.155  -2.450  -0.376   0.215  N7      KYK  29  
KYK  N6      N5   N  0  1  N  N  N  -12.333  24.525  -34.617  -5.501  -0.475  -0.154  N6      KYK  30  
KYK  C2      C15  C  0  1  Y  N  N  -13.857  22.638  -37.151  -4.474   2.783  -1.210  C2      KYK  31  
KYK  C23     C16  C  0  1  Y  N  N  -10.279  27.892  -32.391  -8.326  -3.912  -0.555  C23     KYK  32  
KYK  C25     C17  C  0  1  Y  N  N  -11.024  25.663  -32.934  -7.582  -1.711   0.023  C25     KYK  33  
KYK  C27     C18  C  0  1  Y  N  N   -8.670  26.163  -32.758  -8.602  -3.103   1.682  C27     KYK  34  
KYK  H8      H1   H  0  1  N  N  N  -15.108  20.752  -32.255  -0.357  -0.436   0.514  H8      KYK  35  
KYK  H3      H2   H  0  1  N  N  N  -13.062  25.038  -32.729  -7.367   0.402   0.233  H3      KYK  36  
KYK  H1      H3   H  0  1  N  N  N  -11.863  23.700  -32.757  -7.147  -0.206  -1.426  H1      KYK  37  
KYK  H21     H4   H  0  1  N  N  N   -8.164  28.181  -32.259  -9.212  -5.045   1.027  H21     KYK  38  
KYK  H23     H5   H  0  1  N  N  N  -12.329  27.323  -32.577  -7.405  -2.560  -1.931  H23     KYK  39  
KYK  H25     H6   H  0  1  N  N  N   -9.457  24.246  -33.283  -7.897  -1.120   2.053  H25     KYK  40  
KYK  H4      H7   H  0  1  N  N  N  -18.393  21.206  -29.297   7.896  -4.283  -1.360  H4      KYK  41  
KYK  H5      H8   H  0  1  N  N  N  -15.248  20.102  -28.231   5.543  -3.980   0.722  H5      KYK  42  
KYK  H6      H9   H  0  1  N  N  N  -20.994  17.839  -30.324   6.728   1.051  -0.025  H6      KYK  43  
KYK  H3A2    H10  H  0  0  N  N  N  -17.934  17.545  -28.195   5.830  -0.964  -1.872  H3A2    KYK  44  
KYK  H3A1    H11  H  0  0  N  N  N  -16.748  17.405  -29.537   4.613  -2.102  -1.248  H3A1    KYK  45  
KYK  "H5'2"  H12  H  0  0  N  N  N  -17.143  16.478  -32.055   2.809   1.107   1.524  "H5'2"  KYK  46  
KYK  "H5'1"  H13  H  0  0  N  N  N  -16.247  17.950  -31.547   4.024   2.314   1.040  "H5'1"  KYK  47  
KYK  "H4'"   H14  H  0  1  N  N  N  -17.627  17.469  -34.219   2.645   2.792  -1.018  "H4'"   KYK  48  
KYK  "H3'"   H15  H  0  1  N  N  N  -14.735  17.644  -33.301   2.041   3.472   1.755  "H3'"   KYK  49  
KYK  "HO3'"  H16  H  0  0  N  N  N  -15.723  15.580  -33.613   1.471   5.510   0.648  "HO3'"  KYK  50  
KYK  "H2'"   H17  H  0  1  N  N  N  -14.141  18.620  -35.357  -0.152   2.630   1.725  "H2'"   KYK  51  
KYK  "HO2'"  H18  H  0  0  N  N  N  -15.356  17.176  -36.753  -0.608   4.957   1.442  "HO2'"  KYK  52  
KYK  "H1'"   H19  H  0  1  N  N  N  -16.562  20.026  -35.676  -0.181   2.854  -1.340  "H1'"   KYK  53  
KYK  HN61    H20  H  0  0  N  N  N  -11.417  24.431  -35.006  -5.103  -1.288   0.196  HN61    KYK  54  
KYK  H2      H21  H  0  1  N  N  N  -13.866  22.689  -38.230  -4.944   3.674  -1.599  H2      KYK  55  
KYK  H22     H22  H  0  1  N  N  N  -10.510  28.921  -32.158  -8.449  -4.696  -1.288  H22     KYK  56  
KYK  H26     H23  H  0  1  N  N  N   -7.642  25.834  -32.797  -8.937  -3.257   2.697  H26     KYK  57  
#   #
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
KYK  C2     N3      DOUB  Y  N   1  
KYK  C2     N1      SING  Y  N   2  
KYK  N3     C4      SING  Y  N   3  
KYK  N1     C6      DOUB  Y  N   4  
KYK  "O2'"  "C2'"   SING  N  N   5  
KYK  C4     C5      DOUB  Y  N   6  
KYK  C4     N9      SING  Y  N   7  
KYK  "C2'"  "C1'"   SING  N  N   8  
KYK  "C2'"  "C3'"   SING  N  N   9  
KYK  C6     N6      SING  N  N  10  
KYK  C6     C5      SING  Y  N  11  
KYK  "C1'"  N9      SING  N  N  12  
KYK  "C1'"  "O4'"   SING  N  N  13  
KYK  N6     C21     SING  N  N  14  
KYK  C5     N7      SING  Y  N  15  
KYK  N9     C8      SING  Y  N  16  
KYK  "O3'"  "C3'"   SING  N  N  17  
KYK  "C3'"  "C4'"   SING  N  N  18  
KYK  "O4'"  "C4'"   SING  N  N  19  
KYK  "C4'"  "C5'"   SING  N  N  20  
KYK  C21    C25     SING  N  N  21  
KYK  C8     N7      DOUB  Y  N  22  
KYK  C26    C25     DOUB  Y  N  23  
KYK  C26    C27     SING  Y  N  24  
KYK  C25    C24     SING  Y  N  25  
KYK  C27    C22     DOUB  Y  N  26  
KYK  C24    C23     DOUB  Y  N  27  
KYK  C22    C23     SING  Y  N  28  
KYK  "C5'"  "O5'"   SING  N  N  29  
KYK  "O5'"  PA      SING  N  N  30  
KYK  O2A    PA      DOUB  N  N  31  
KYK  PA     O1A     SING  N  N  32  
KYK  PA     C3A     SING  N  N  33  
KYK  O3B    PB      DOUB  N  N  34  
KYK  C3A    PB      SING  N  N  35  
KYK  PB     O1B     SING  N  N  36  
KYK  PB     O2B     SING  N  N  37  
KYK  C8     H8      SING  N  N  38  
KYK  C21    H3      SING  N  N  39  
KYK  C21    H1      SING  N  N  40  
KYK  C22    H21     SING  N  N  41  
KYK  C24    H23     SING  N  N  42  
KYK  C26    H25     SING  N  N  43  
KYK  O1B    H4      SING  N  N  44  
KYK  O2B    H5      SING  N  N  45  
KYK  O1A    H6      SING  N  N  46  
KYK  C3A    H3A2    SING  N  N  47  
KYK  C3A    H3A1    SING  N  N  48  
KYK  "C5'"  "H5'2"  SING  N  N  49  
KYK  "C5'"  "H5'1"  SING  N  N  50  
KYK  "C4'"  "H4'"   SING  N  N  51  
KYK  "C3'"  "H3'"   SING  N  N  52  
KYK  "O3'"  "HO3'"  SING  N  N  53  
KYK  "C2'"  "H2'"   SING  N  N  54  
KYK  "O2'"  "HO2'"  SING  N  N  55  
KYK  "C1'"  "H1'"   SING  N  N  56  
KYK  N6     HN61    SING  N  N  57  
KYK  C2     H2      SING  N  N  58  
KYK  C23    H22     SING  N  N  59  
KYK  C27    H26     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
KYK  InChI             InChI                 1.03   "InChI=1S/C18H23N5O9P2/c24-14-12(7-31-34(29,30)10-33(26,27)28)32-18(15(14)25)23-9-22-13-16(20-8-21-17(13)23)19-6-11-4-2-1-3-5-11/h1-5,8-9,12,14-15,18,24-25H,6-7,10H2,(H,29,30)(H,19,20,21)(H2,26,27,28)/t12-,14-,15-,18-/m1/s1"  
KYK  InChIKey          InChI                 1.03   DMBYYIJBPDWQFF-SCFUHWHPSA-N  
KYK  SMILES_CANONICAL  CACTVS                3.385  "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)C[P](O)(O)=O)n2cnc3c(NCc4ccccc4)ncnc23"  
KYK  SMILES            CACTVS                3.385  "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)C[P](O)(O)=O)n2cnc3c(NCc4ccccc4)ncnc23"  
KYK  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1ccc(cc1)CNc2c3c(ncn2)n(cn3)[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(CP(=O)(O)O)O)O)O"  
KYK  SMILES            "OpenEye OEToolkits"  2.0.7  "c1ccc(cc1)CNc2c3c(ncn2)n(cn3)C4C(C(C(O4)COP(=O)(CP(=O)(O)O)O)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          KYK
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.7
_pdbx_chem_comp_identifier.identifier       "[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-[6-[(phenylmethyl)amino]purin-9-yl]oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
KYK  "Create component"  2019-07-05  EBI   
KYK  "Initial release"   2020-07-22  RCSB  
##
