data_J0X
#

_chem_comp.id                                   J0X
_chem_comp.name                                 "2-[[2-oxidanylidene-1-[(2R,4S,5R)-4-oxidanyl-5-(phosphonooxymethyl)oxolan-2-yl]pyrimidin-4-yl]amino]ethanoic acid"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C11 H16 N3 O9 P"
_chem_comp.mon_nstd_parent_comp_id              DC
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-03-17
_chem_comp.pdbx_modified_date                   2022-03-04
_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                       365.233
_chem_comp.one_letter_code                      C
_chem_comp.three_letter_code                    J0X
_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       7EAY
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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
J0X  "C1'"  C1   C  0  1  N  N  R  21.388  -33.565  -24.466   0.305   1.951  -0.808  "C1'"  J0X   1  
J0X  C2     C2   C  0  1  N  N  N  20.816  -34.829  -26.455  -1.398   0.575   0.253  C2     J0X   2  
J0X  "C2'"  C3   C  0  1  N  N  N  22.890  -33.237  -24.329   0.536   2.885   0.395  "C2'"  J0X   3  
J0X  "C3'"  C4   C  0  1  N  N  S  22.918  -32.549  -22.965   1.754   2.268   1.126  "C3'"  J0X   4  
J0X  C4     C5   C  0  1  N  N  N  20.268  -33.750  -28.410  -3.531   0.331  -0.601  C4     J0X   5  
J0X  "C4'"  C6   C  0  1  N  N  R  21.814  -31.821  -22.967   2.404   1.413   0.008  "C4'"  J0X   6  
J0X  C5     C7   C  0  1  N  N  N  20.448  -32.522  -27.837  -3.199   1.189  -1.669  C5     J0X   7  
J0X  "C5'"  C8   C  0  1  N  N  N  21.991  -30.374  -23.494   3.232   0.276   0.611  "C5'"  J0X   8  
J0X  C6     C9   C  0  1  N  N  N  20.821  -32.503  -26.498  -1.952   1.716  -1.725  C6     J0X   9  
J0X  C7     C10  C  0  1  N  N  N  19.163  -32.932  -31.918  -6.558  -1.569   0.447  C7     J0X  10  
J0X  C8     C11  C  0  1  N  N  N  19.753  -32.559  -30.541  -5.131  -1.108   0.592  C8     J0X  11  
J0X  N1     N1   N  0  1  N  N  N  21.002  -33.644  -25.854  -1.051   1.396  -0.754  N1     J0X  12  
J0X  N3     N2   N  0  1  N  N  N  20.466  -34.876  -27.710  -2.621   0.053   0.324  N3     J0X  13  
J0X  N4     N3   N  0  1  N  N  N  19.856  -33.812  -29.835  -4.790  -0.217  -0.520  N4     J0X  14  
J0X  O2     O1   O  0  1  N  N  N  20.975  -35.887  -25.842  -0.577   0.299   1.112  O2     J0X  15  
J0X  "O3'"  O2   O  0  1  N  N  N  22.777  -33.684  -22.019   2.650   3.286   1.574  "O3'"  J0X  16  
J0X  "O4'"  O3   O  0  1  N  N  N  20.749  -32.559  -23.924   1.271   0.891  -0.719  "O4'"  J0X  17  
J0X  "O5'"  O4   O  0  1  N  N  N  22.943  -30.318  -24.563   3.912  -0.424  -0.433  "O5'"  J0X  18  
J0X  O8     O5   O  0  1  N  N  N  18.880  -32.050  -32.743  -7.223  -1.192  -0.489  O8     J0X  19  
J0X  O9     O6   O  0  1  N  N  N  18.969  -34.129  -32.179  -7.091  -2.398   1.358  O9     J0X  20  
J0X  OP1    O7   O  0  1  N  N  N  21.451  -29.261  -26.310   5.922  -1.301   0.817  OP1    J0X  21  
J0X  OP2    O8   O  0  1  N  N  N  22.833  -27.755  -24.857   4.011  -2.905   0.431  OP2    J0X  22  
J0X  P      P1   P  0  1  N  N  N  22.737  -29.046  -25.585   4.877  -1.683  -0.160  P      J0X  23  
J0X  H1     H1   H  0  1  N  N  N  21.182  -34.518  -23.957   0.445   2.503  -1.738  H1     J0X  24  
J0X  H2     H2   H  0  1  N  N  N  23.504  -34.149  -24.333   0.767   3.895   0.056  H2     J0X  25  
J0X  H3     H3   H  0  1  N  N  N  23.230  -32.562  -25.128  -0.337   2.891   1.048  H3     J0X  26  
J0X  H4     H4   H  0  1  N  N  N  23.852  -31.988  -22.811   1.432   1.641   1.957  H4     J0X  27  
J0X  H5     H5   H  0  1  N  N  N  21.370  -31.766  -21.962   3.022   2.034  -0.640  H5     J0X  28  
J0X  H6     H6   H  0  1  N  N  N  20.307  -31.610  -28.398  -3.928   1.426  -2.430  H6     J0X  29  
J0X  H7     H7   H  0  1  N  N  N  22.340  -29.734  -22.670   3.961   0.689   1.308  H7     J0X  30  
J0X  H8     H8   H  0  1  N  N  N  21.021  -30.005  -23.859   2.573  -0.412   1.141  H8     J0X  31  
J0X  H9     H9   H  0  1  N  N  N  20.962  -31.562  -25.987  -1.674   2.375  -2.533  H9     J0X  32  
J0X  H10    H10  H  0  1  N  N  N  20.744  -32.096  -30.656  -5.016  -0.573   1.535  H10    J0X  33  
J0X  H11    H11  H  0  1  N  N  N  19.085  -31.867  -30.007  -4.467  -1.972   0.582  H11    J0X  34  
J0X  H12    H12  H  0  1  N  N  N  19.659  -34.683  -30.285  -5.452  -0.014  -1.199  H12    J0X  35  
J0X  H13    H13  H  0  1  N  N  N  22.783  -33.356  -21.127   2.259   3.902   2.209  H13    J0X  36  
J0X  H14    H14  H  0  1  N  N  N  18.599  -34.208  -33.050  -8.011  -2.666   1.223  H14    J0X  37  
J0X  H16    H16  H  0  1  N  N  N  22.030  -27.262  -24.978   3.306  -3.208  -0.157  H16    J0X  38  
J0X  OP3    O9   O  0  1  N  Y  N  23.908  -29.161  -26.663   5.571  -2.136  -1.540  O1     J0X  39  
J0X  H15    H15  H  0  1  N  Y  N  23.535  -29.339  -27.519   6.168  -2.892  -1.450  H15    J0X  40  
#   #
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
J0X  O8     C7     DOUB  N  N   1  
J0X  O9     C7     SING  N  N   2  
J0X  C7     C8     SING  N  N   3  
J0X  C8     N4     SING  N  N   4  
J0X  N4     C4     SING  N  N   5  
J0X  C4     C5     SING  N  N   6  
J0X  C4     N3     DOUB  N  N   7  
J0X  C5     C6     DOUB  N  N   8  
J0X  N3     C2     SING  N  N   9  
J0X  C6     N1     SING  N  N  10  
J0X  C2     N1     SING  N  N  11  
J0X  C2     O2     DOUB  N  N  12  
J0X  OP1    P      DOUB  N  N  13  
J0X  N1     "C1'"  SING  N  N  14  
J0X  P      OP2    SING  N  N  15  
J0X  P      "O5'"  SING  N  N  16  
J0X  "O5'"  "C5'"  SING  N  N  17  
J0X  "C1'"  "C2'"  SING  N  N  18  
J0X  "C1'"  "O4'"  SING  N  N  19  
J0X  "C2'"  "C3'"  SING  N  N  20  
J0X  "O4'"  "C4'"  SING  N  N  21  
J0X  "C5'"  "C4'"  SING  N  N  22  
J0X  "C4'"  "C3'"  SING  N  N  23  
J0X  "C3'"  "O3'"  SING  N  N  24  
J0X  "C1'"  H1     SING  N  N  25  
J0X  "C2'"  H2     SING  N  N  26  
J0X  "C2'"  H3     SING  N  N  27  
J0X  "C3'"  H4     SING  N  N  28  
J0X  "C4'"  H5     SING  N  N  29  
J0X  C5     H6     SING  N  N  30  
J0X  "C5'"  H7     SING  N  N  31  
J0X  "C5'"  H8     SING  N  N  32  
J0X  C6     H9     SING  N  N  33  
J0X  C8     H10    SING  N  N  34  
J0X  C8     H11    SING  N  N  35  
J0X  N4     H12    SING  N  N  36  
J0X  "O3'"  H13    SING  N  N  37  
J0X  O9     H14    SING  N  N  38  
J0X  OP2    H16    SING  N  N  39  
J0X  P      OP3    SING  N  N  40  
J0X  OP3    H15    SING  N  N  41  
#   #
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
J0X  InChI             InChI                 1.03   "InChI=1S/C11H16N3O9P/c15-6-3-9(23-7(6)5-22-24(19,20)21)14-2-1-8(13-11(14)18)12-4-10(16)17/h1-2,6-7,9,15H,3-5H2,(H,16,17)(H,12,13,18)(H2,19,20,21)/t6-,7+,9+/m0/s1"  
J0X  InChIKey          InChI                 1.03   QYPVHBKFTXARRD-LKEWCRSYSA-N  
J0X  SMILES_CANONICAL  CACTVS                3.385  "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=NC2=O)NCC(O)=O"  
J0X  SMILES            CACTVS                3.385  "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=NC2=O)NCC(O)=O"  
J0X  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)NCC(=O)O)COP(=O)(O)O)O"  
J0X  SMILES            "OpenEye OEToolkits"  2.0.7  "C1C(C(OC1N2C=CC(=NC2=O)NCC(=O)O)COP(=O)(O)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          J0X
_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-[[2-oxidanylidene-1-[(2~{R},4~{S},5~{R})-4-oxidanyl-5-(phosphonooxymethyl)oxolan-2-yl]pyrimidin-4-yl]amino]ethanoic 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
J0X  "Create component"  2021-03-17  PDBJ  
J0X  "Initial release"   2022-03-09  RCSB  
##
