data_OKN
#

_chem_comp.id                                   OKN
_chem_comp.name                                 "5'-methyl-2'-deoxycytidine-5'-phosphorothioate"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C10 H16 N3 O6 P S"
_chem_comp.mon_nstd_parent_comp_id              DC
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-03-19
_chem_comp.pdbx_modified_date                   2020-04-24
_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                       337.289
_chem_comp.one_letter_code                      C
_chem_comp.three_letter_code                    OKN
_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       6YCS
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBE
#   #
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
OKN  C2      C1   C  0  1  N  N  N   -7.939  -29.442  39.268  -2.439  -0.252   0.804  C2     OKN   1  
OKN  C4      C2   C  0  1  N  N  N  -10.219  -29.256  38.931  -4.468  -1.293   0.433  C4     OKN   2  
OKN  "C1'"   C3   C  0  1  N  N  R   -6.377  -29.555  37.466  -1.417   1.267  -0.798  "C1'"  OKN   3  
OKN  "C2'"   C4   C  0  1  N  N  N   -6.317  -30.497  36.142  -1.358   2.483   0.146  "C2'"  OKN   4  
OKN  "C3'"   C5   C  0  1  N  N  S   -5.334  -30.117  35.529   0.073   2.438   0.735  "C3'"  OKN   5  
OKN  "C4'"   C6   C  0  1  N  N  R   -5.253  -28.555  35.826   0.826   1.572  -0.308  "C4'"  OKN   6  
OKN  C5      C7   C  0  1  N  N  N  -10.019  -29.267  37.564  -4.565  -0.652  -0.819  C5     OKN   7  
OKN  "C5'"   C8   C  0  1  N  N  N   -5.853  -27.821  34.769   2.042   0.896   0.329  "C5'"  OKN   8  
OKN  C6      C9   C  0  1  N  N  N   -8.723  -29.370  37.107  -3.565   0.170  -1.215  C6     OKN   9  
OKN  CM5     C10  C  0  1  N  N  N  -11.186  -29.168  36.588  -5.759  -0.888  -1.709  CM5    OKN  10  
OKN  N1      N1   N  0  1  N  N  N   -7.719  -29.458  37.959  -2.500   0.370  -0.388  N1     OKN  11  
OKN  N3      N2   N  0  1  N  N  N   -9.177  -29.344  39.736  -3.410  -1.072   1.202  N3     OKN  12  
OKN  N4      N3   N  0  1  N  N  N  -11.558  -29.150  39.482  -5.465  -2.142   0.855  N4     OKN  13  
OKN  O2      O1   O  0  1  N  N  N   -7.028  -29.519  40.021  -1.477  -0.065   1.530  O2     OKN  14  
OKN  "O3'"   O2   O  0  1  N  N  N   -4.092  -30.779  36.089   0.637   3.748   0.811  "O3'"  OKN  15  
OKN  "O4'"   O3   O  0  1  N  N  N   -5.977  -28.368  37.089  -0.155   0.585  -0.701  "O4'"  OKN  16  
OKN  "O5'"   O4   O  0  1  N  N  N   -5.158  -28.155  33.602   2.782   0.200  -0.676  "O5'"  OKN  17  
OKN  OP1     O5   O  0  1  N  N  N   -5.618  -29.248  31.209   5.101   0.258   0.317  OP1    OKN  18  
OKN  P       P1   P  0  1  N  N  N   -5.850  -27.904  32.130   4.127  -0.626  -0.361  P      OKN  19  
OKN  S01     S1   S  0  1  N  N  N   -7.841  -27.587  32.347   3.668  -2.269   0.899  S01    OKN  20  
OKN  OP3     O6   O  0  1  N  Y  N   -4.584  -27.211  31.545   4.760  -1.167  -1.738  O1     OKN  21  
OKN  H1      H1   H  0  1  N  N  N   -5.719  -29.999  38.228  -1.580   1.600  -1.823  H1     OKN  22  
OKN  H2      H2   H  0  1  N  N  N   -7.225  -30.369  35.535  -1.511   3.407  -0.412  H2     OKN  23  
OKN  H3      H3   H  0  1  N  N  N   -6.211  -31.555  36.425  -2.101   2.389   0.938  H3     OKN  24  
OKN  H4      H4   H  0  1  N  N  N   -5.379  -30.269  34.441   0.076   1.957   1.713  H4     OKN  25  
OKN  H5      H5   H  0  1  N  N  N   -4.196  -28.276  35.948   1.126   2.176  -1.164  H5     OKN  26  
OKN  H6      H6   H  0  1  N  N  N   -5.771  -26.741  34.963   2.678   1.653   0.790  H6     OKN  27  
OKN  H7      H7   H  0  1  N  N  N   -6.913  -28.096  34.671   1.708   0.190   1.089  H7     OKN  28  
OKN  H8      H8   H  0  1  N  N  N   -8.528  -29.379  36.045  -3.616   0.672  -2.170  H8     OKN  29  
OKN  H9      H9   H  0  1  N  N  N  -12.129  -29.094  37.149  -6.443  -1.582  -1.222  H9     OKN  30  
OKN  H10     H10  H  0  1  N  N  N  -11.063  -28.274  35.959  -6.269   0.058  -1.892  H10    OKN  31  
OKN  H11     H11  H  0  1  N  N  N  -11.208  -30.064  35.951  -5.426  -1.310  -2.658  H11    OKN  32  
OKN  H12     H12  H  0  1  N  N  N  -11.692  -29.144  40.473  -5.396  -2.581   1.717  H12    OKN  33  
OKN  H13     H13  H  0  1  N  N  N  -12.346  -29.083  38.871  -6.238  -2.301   0.290  H13    OKN  34  
OKN  H14     H14  H  0  1  N  N  N   -4.126  -31.713  35.919   0.200   4.328   1.450  H14    OKN  35  
OKN  H15     H15  H  0  1  N  N  N   -8.347  -28.575  31.670   2.787  -2.974   0.167  H15    OKN  36  
OKN  HOP3    H16  H  0  0  N  Y  N   -4.172  -27.786  30.911   5.574  -1.675  -1.624  H16    OKN  37  
#   #
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
OKN  OP1    P       DOUB  N  N   1  
OKN  P      S01     SING  N  N   2  
OKN  P      "O5'"   SING  N  N   3  
OKN  "O5'"  "C5'"   SING  N  N   4  
OKN  "C5'"  "C4'"   SING  N  N   5  
OKN  "C3'"  "C4'"   SING  N  N   6  
OKN  "C3'"  "O3'"   SING  N  N   7  
OKN  "C3'"  "C2'"   SING  N  N   8  
OKN  "C4'"  "O4'"   SING  N  N   9  
OKN  "C2'"  "C1'"   SING  N  N  10  
OKN  CM5    C5      SING  N  N  11  
OKN  "O4'"  "C1'"   SING  N  N  12  
OKN  C6     C5      DOUB  N  N  13  
OKN  C6     N1      SING  N  N  14  
OKN  "C1'"  N1      SING  N  N  15  
OKN  C5     C4      SING  N  N  16  
OKN  N1     C2      SING  N  N  17  
OKN  C4     N4      SING  N  N  18  
OKN  C4     N3      DOUB  N  N  19  
OKN  C2     N3      SING  N  N  20  
OKN  C2     O2      DOUB  N  N  21  
OKN  P      OP3     SING  N  N  22  
OKN  "C1'"  H1      SING  N  N  23  
OKN  "C2'"  H2      SING  N  N  24  
OKN  "C2'"  H3      SING  N  N  25  
OKN  "C3'"  H4      SING  N  N  26  
OKN  "C4'"  H5      SING  N  N  27  
OKN  "C5'"  H6      SING  N  N  28  
OKN  "C5'"  H7      SING  N  N  29  
OKN  C6     H8      SING  N  N  30  
OKN  CM5    H9      SING  N  N  31  
OKN  CM5    H10     SING  N  N  32  
OKN  CM5    H11     SING  N  N  33  
OKN  N4     H12     SING  N  N  34  
OKN  N4     H13     SING  N  N  35  
OKN  "O3'"  H14     SING  N  N  36  
OKN  S01    H15     SING  N  N  37  
OKN  OP3    HOP3    SING  N  N  38  
#   #
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
OKN  InChI             InChI                 1.03   "InChI=1S/C10H16N3O6PS/c1-5-3-13(10(15)12-9(5)11)8-2-6(14)7(19-8)4-18-20(16,17)21/h3,6-8,14H,2,4H2,1H3,(H2,11,12,15)(H2,16,17,21)/t6-,7+,8+/m0/s1"  
OKN  InChIKey          InChI                 1.03   UZWQYGFEEXJOHY-XLPZGREQSA-N  
OKN  SMILES_CANONICAL  CACTVS                3.385  "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(S)=O)O2)C(=O)N=C1N"  
OKN  SMILES            CACTVS                3.385  "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(S)=O)O2)C(=O)N=C1N"  
OKN  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CC1=CN(C(=O)N=C1N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)S)O"  
OKN  SMILES            "OpenEye OEToolkits"  2.0.7  "CC1=CN(C(=O)N=C1N)C2CC(C(O2)COP(=O)(O)S)O"  
#
_pdbx_chem_comp_identifier.comp_id          OKN
_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},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphinic 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
OKN  "Create component"  2020-03-19  PDBE  
OKN  "Initial release"   2020-04-29  RCSB  
##
