data_J4T
#

_chem_comp.id                                   J4T
_chem_comp.name                                 "[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-4-[1-[(2,2,5,5-tetramethyl-1-oxidanyl-pyrrol-3-yl)methyl]-1,2,3-triazol-4-yl]oxolan-2-yl]methyl dihydrogen phosphate"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C20 H29 N6 O9 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2019-01-25
_chem_comp.pdbx_modified_date                   2020-02-07
_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                       528.453
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    J4T
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  Y
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       6QJR
_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
J4T  P      P1   P  0  1  N  N  N   -5.917  11.923  -7.418   6.340  -1.886   0.755  P      J4T   1  
J4T  OP1    O1   O  0  1  N  N  N   -5.176  11.257  -6.289   7.181  -0.914   0.020  OP1    J4T   2  
J4T  "O5'"  O2   O  0  1  N  N  N   -7.336  11.269  -7.705   4.794  -1.455   0.638  "O5'"  J4T   3  
J4T  "C5'"  C1   C  0  1  N  N  N   -8.395  11.506  -6.802   4.138  -1.243  -0.614  "C5'"  J4T   4  
J4T  "C4'"  C2   C  0  1  N  N  R   -9.077  10.187  -6.447   2.681  -0.845  -0.365  "C4'"  J4T   5  
J4T  "C3'"  C3   C  0  1  N  N  S   -9.163   9.984  -4.978   1.919  -0.733  -1.704  "C3'"  J4T   6  
J4T  "O3'"  O3   O  0  1  N  N  N  -10.192  10.783  -4.462   1.172  -1.924  -1.957  "O3'"  J4T   7  
J4T  "C2'"  C4   C  0  1  N  N  R   -9.391   8.494  -4.802   0.969   0.468  -1.495  "C2'"  J4T   8  
J4T  "C1'"  C5   C  0  1  N  N  R   -8.764   7.898  -6.042   1.270   0.938  -0.055  "C1'"  J4T   9  
J4T  "O4'"  O4   O  0  1  N  N  N   -8.379   9.016  -6.879   2.612   0.477   0.211  "O4'"  J4T  10  
J4T  N1     N1   N  0  1  N  N  N   -7.606   7.006  -5.829   1.207   2.400   0.028  N1     J4T  11  
J4T  C6     C6   C  0  1  N  N  N   -6.363   7.488  -5.884   2.111   3.157  -0.666  C6     J4T  12  
J4T  C5     C7   C  0  1  N  N  N   -5.285   6.623  -5.781   2.053   4.504  -0.590  C5     J4T  13  
J4T  C4     C8   C  0  1  N  N  N   -5.510   5.263  -5.651   1.052   5.106   0.211  C4     J4T  14  
J4T  N3     N2   N  0  1  N  N  N   -6.745   4.784  -5.620   0.180   4.325   0.879  N3     J4T  15  
J4T  C2     C9   C  0  1  N  N  N   -7.793   5.604  -5.719   0.257   2.984   0.781  C2     J4T  16  
J4T  O2     O5   O  0  1  N  N  N   -8.945   5.118  -5.686  -0.539   2.292   1.385  O2     J4T  17  
J4T  O4     O6   O  0  1  N  N  N   -4.548   4.483  -5.558   0.980   6.319   0.296  O4     J4T  18  
J4T  OP2    O7   O  0  1  N  N  N   -6.105  13.407  -7.231   6.538  -3.353   0.122  OP2    J4T  19  
J4T  C3     C10  C  0  1  Y  N  N  -10.857   8.156  -4.766  -0.469   0.032  -1.619  C3     J4T  20  
J4T  C7     C11  C  0  1  Y  N  N  -11.182   6.871  -4.337  -0.986  -1.165  -1.255  C7     J4T  21  
J4T  N8     N3   N  0  1  Y  N  N  -12.528   6.761  -4.365  -2.306  -1.110  -1.548  N8     J4T  22  
J4T  N9     N4   N  0  1  Y  N  N  -13.062   7.981  -4.830  -2.559   0.046  -2.053  N9     J4T  23  
J4T  N10    N5   N  0  1  Y  N  N  -11.975   8.849  -5.082  -1.485   0.753  -2.104  N10    J4T  24  
J4T  H2     H2   H  0  1  N  N  N   -7.998  11.970  -5.887   4.644  -0.446  -1.159  H2     J4T  25  
J4T  H3     H3   H  0  1  N  N  N   -9.127  12.182  -7.267   4.169  -2.161  -1.201  H3     J4T  26  
J4T  H4     H4   H  0  1  N  N  N  -10.093  10.194  -6.869   2.197  -1.571   0.287  H4     J4T  27  
J4T  H5     H5   H  0  1  N  N  N   -8.201  10.252  -4.518   2.611  -0.534  -2.522  H5     J4T  28  
J4T  H6     H6   H  0  1  N  N  N  -10.251  10.656  -3.522   1.715  -2.720  -2.036  H6     J4T  29  
J4T  H7     H7   H  0  1  N  N  N   -8.884   8.129  -3.897   1.189   1.259  -2.212  H7     J4T  30  
J4T  H8     H8   H  0  1  N  N  N   -9.543   7.325  -6.566   0.566   0.489   0.646  H8     J4T  31  
J4T  H9     H9   H  0  1  N  N  N   -6.198   8.548  -6.008   2.867   2.680  -1.271  H9     J4T  32  
J4T  H10    H10  H  0  1  N  N  N   -4.276   7.007  -5.802   2.760   5.114  -1.132  H10    J4T  33  
J4T  H11    H11  H  0  1  N  N  N   -6.893   3.800  -5.522  -0.508   4.730   1.429  H11    J4T  34  
J4T  H12    H12  H  0  1  N  N  N   -5.712  13.675  -6.409   6.016  -4.042   0.556  H12    J4T  35  
J4T  H13    H13  H  0  1  N  N  N  -10.485   6.103  -4.037  -0.452  -1.997  -0.820  H13    J4T  36  
J4T  O1     O8   O  0  1  N  N  N        ?       ?       ?   6.776  -1.907   2.305  O1     J4T  37  
J4T  C1     C12  C  0  1  N  N  N        ?       ?       ?  -3.279  -2.182  -1.327  C1     J4T  38  
J4T  C12    C33  C  0  1  N  N  N        ?       ?       ?  -4.421  -1.661  -0.493  C12    J4T  39  
J4T  C8     C14  C  0  1  N  N  N        ?       ?       ?  -4.439  -1.593   1.017  C8     J4T  40  
J4T  N2     N6   N  0  1  N  N  N        ?       ?       ?  -5.865  -1.422   1.385  N2     J4T  41  
J4T  C10    C15  C  0  1  N  N  N        ?       ?       ?  -6.438  -0.771   0.184  C10    J4T  42  
J4T  C11    C16  C  0  1  N  N  N        ?       ?       ?  -5.549  -1.190  -0.964  C11    J4T  43  
J4T  C9     C17  C  0  1  N  N  N        ?       ?       ?  -7.871  -1.253  -0.048  C9     J4T  44  
J4T  C13    C13  C  0  1  N  N  N        ?       ?       ?  -6.408   0.751   0.341  C13    J4T  45  
J4T  C14    C19  C  0  1  N  N  N        ?       ?       ?  -3.889  -2.891   1.612  C14    J4T  46  
J4T  C15    C20  C  0  1  N  N  N        ?       ?       ?  -3.619  -0.396   1.503  C15    J4T  47  
J4T  O3     O9   O  0  1  N  N  N        ?       ?       ?  -6.003  -0.565   2.563  O3     J4T  48  
J4T  H1     H1   H  0  1  N  N  N        ?       ?       ?   7.698  -2.159   2.451  H1     J4T  49  
J4T  H14    H14  H  0  1  N  N  N        ?       ?       ?  -3.660  -2.530  -2.287  H14    J4T  50  
J4T  H15    H15  H  0  1  N  N  N        ?       ?       ?  -2.797  -3.010  -0.806  H15    J4T  51  
J4T  H16    H16  H  0  1  N  N  N        ?       ?       ?  -5.806  -1.120  -2.011  H16    J4T  52  
J4T  H17    H17  H  0  1  N  N  N        ?       ?       ?  -8.483  -1.002   0.819  H17    J4T  53  
J4T  H18    H18  H  0  1  N  N  N        ?       ?       ?  -8.280  -0.766  -0.933  H18    J4T  54  
J4T  H19    H19  H  0  1  N  N  N        ?       ?       ?  -7.872  -2.333  -0.194  H19    J4T  55  
J4T  H20    H20  H  0  1  N  N  N        ?       ?       ?  -5.374   1.095   0.350  H20    J4T  56  
J4T  H21    H21  H  0  1  N  N  N        ?       ?       ?  -6.937   1.213  -0.493  H21    J4T  57  
J4T  H22    H22  H  0  1  N  N  N        ?       ?       ?  -6.892   1.029   1.277  H22    J4T  58  
J4T  H23    H23  H  0  1  N  N  N        ?       ?       ?  -2.864  -3.039   1.274  H23    J4T  59  
J4T  H24    H24  H  0  1  N  N  N        ?       ?       ?  -3.908  -2.828   2.700  H24    J4T  60  
J4T  H25    H25  H  0  1  N  N  N        ?       ?       ?  -4.504  -3.729   1.286  H25    J4T  61  
J4T  H26    H26  H  0  1  N  N  N        ?       ?       ?  -3.971   0.510   1.011  H26    J4T  62  
J4T  H27    H27  H  0  1  N  N  N        ?       ?       ?  -3.734  -0.292   2.582  H27    J4T  63  
J4T  H28    H28  H  0  1  N  N  N        ?       ?       ?  -2.567  -0.555   1.264  H28    J4T  64  
J4T  H29    H29  H  0  1  N  N  N        ?       ?       ?  -6.918  -0.425   2.842  H29    J4T  65  
#   #
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
J4T  "O5'"  P      SING  N  N   1  
J4T  "O5'"  "C5'"  SING  N  N   2  
J4T  P      OP2    SING  N  N   3  
J4T  P      OP1    DOUB  N  N   4  
J4T  "O4'"  "C4'"  SING  N  N   5  
J4T  "O4'"  "C1'"  SING  N  N   6  
J4T  "C5'"  "C4'"  SING  N  N   7  
J4T  "C4'"  "C3'"  SING  N  N   8  
J4T  "C1'"  N1     SING  N  N   9  
J4T  "C1'"  "C2'"  SING  N  N  10  
J4T  C6     N1     SING  N  N  11  
J4T  C6     C5     DOUB  N  N  12  
J4T  N1     C2     SING  N  N  13  
J4T  C5     C4     SING  N  N  14  
J4T  C2     O2     DOUB  N  N  15  
J4T  C2     N3     SING  N  N  16  
J4T  C4     N3     SING  N  N  17  
J4T  C4     O4     DOUB  N  N  18  
J4T  N10    N9     DOUB  Y  N  19  
J4T  N10    C3     SING  Y  N  20  
J4T  "C3'"  "C2'"  SING  N  N  21  
J4T  "C3'"  "O3'"  SING  N  N  22  
J4T  N9     N8     SING  Y  N  23  
J4T  "C2'"  C3     SING  N  N  24  
J4T  C3     C7     DOUB  Y  N  25  
J4T  N8     C7     SING  Y  N  26  
J4T  "C5'"  H2     SING  N  N  27  
J4T  "C5'"  H3     SING  N  N  28  
J4T  "C4'"  H4     SING  N  N  29  
J4T  "C3'"  H5     SING  N  N  30  
J4T  "O3'"  H6     SING  N  N  31  
J4T  "C2'"  H7     SING  N  N  32  
J4T  "C1'"  H8     SING  N  N  33  
J4T  C6     H9     SING  N  N  34  
J4T  C5     H10    SING  N  N  35  
J4T  N3     H11    SING  N  N  36  
J4T  OP2    H12    SING  N  N  37  
J4T  C7     H13    SING  N  N  38  
J4T  P      O1     SING  N  N  39  
J4T  N8     C1     SING  N  N  40  
J4T  C1     C12    SING  N  N  41  
J4T  C12    C8     SING  N  N  42  
J4T  C8     N2     SING  N  N  43  
J4T  N2     C10    SING  N  N  44  
J4T  C10    C11    SING  N  N  45  
J4T  C11    C12    DOUB  N  N  46  
J4T  C10    C9     SING  N  N  47  
J4T  C10    C13    SING  N  N  48  
J4T  C8     C14    SING  N  N  49  
J4T  C8     C15    SING  N  N  50  
J4T  N2     O3     SING  N  N  51  
J4T  O1     H1     SING  N  N  52  
J4T  C1     H14    SING  N  N  53  
J4T  C1     H15    SING  N  N  54  
J4T  C11    H16    SING  N  N  55  
J4T  C9     H17    SING  N  N  56  
J4T  C9     H18    SING  N  N  57  
J4T  C9     H19    SING  N  N  58  
J4T  C13    H20    SING  N  N  59  
J4T  C13    H21    SING  N  N  60  
J4T  C13    H22    SING  N  N  61  
J4T  C14    H23    SING  N  N  62  
J4T  C14    H24    SING  N  N  63  
J4T  C14    H25    SING  N  N  64  
J4T  C15    H26    SING  N  N  65  
J4T  C15    H27    SING  N  N  66  
J4T  C15    H28    SING  N  N  67  
J4T  O3     H29    SING  N  N  68  
#   #
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
J4T  InChI             InChI                 1.03   "InChI=1S/C20H29N6O9P/c1-19(2)7-11(20(3,4)26(19)30)8-24-9-12(22-23-24)15-16(28)13(10-34-36(31,32)33)35-17(15)25-6-5-14(27)21-18(25)29/h5-7,9,13,15-17,28,30H,8,10H2,1-4H3,(H,21,27,29)(H2,31,32,33)/t13-,15-,16-,17-/m1/s1"  
J4T  InChIKey          InChI                 1.03   PFKJUQRURFIYIT-MWQQHZPXSA-N  
J4T  SMILES_CANONICAL  CACTVS                3.385  "CC1(C)C=C(Cn2cc(nn2)[C@@H]3[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]3N4C=CC(=O)NC4=O)C(C)(C)N1O"  
J4T  SMILES            CACTVS                3.385  "CC1(C)C=C(Cn2cc(nn2)[CH]3[CH](O)[CH](CO[P](O)(O)=O)O[CH]3N4C=CC(=O)NC4=O)C(C)(C)N1O"  
J4T  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "CC1(C=C(C(N1O)(C)C)Cn2cc(nn2)[C@@H]3[C@@H]([C@H](O[C@H]3N4C=CC(=O)NC4=O)COP(=O)(O)O)O)C"  
J4T  SMILES            "OpenEye OEToolkits"  2.0.6  "CC1(C=C(C(N1O)(C)C)Cn2cc(nn2)C3C(C(OC3N4C=CC(=O)NC4=O)COP(=O)(O)O)O)C"  
#
_pdbx_chem_comp_identifier.comp_id          J4T
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.6
_pdbx_chem_comp_identifier.identifier       "[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-4-[1-[(2,2,5,5-tetramethyl-1-oxidanyl-pyrrol-3-yl)methyl]-1,2,3-triazol-4-yl]oxolan-2-yl]methyl dihydrogen 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
J4T  "Create component"  2019-01-25  EBI   
J4T  "Initial release"   2020-02-12  RCSB  
##
