data_OKT
#

_chem_comp.id                                   OKT
_chem_comp.name                                 "2'-O-methyluridine-5'-phosphorothioate"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C10 H15 N2 O8 P S"
_chem_comp.mon_nstd_parent_comp_id              DU
_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                       354.273
_chem_comp.one_letter_code                      U
_chem_comp.three_letter_code                    OKT
_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       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
OKT  C02     C1   C  0  1  N  N  N  11.497  -26.608  40.821   2.872  -3.451   1.311  C02     OKT   1  
OKT  "C1'"   C2   C  0  1  N  N  R  11.494  -27.270  37.854   1.559  -0.732  -0.817  "C1'"   OKT   2  
OKT  C2      C3   C  0  1  N  N  N  13.365  -25.819  37.367   2.457   1.073   0.542  C2      OKT   3  
OKT  "C2'"   C4   C  0  1  N  N  R  10.502  -26.292  38.700   1.464  -1.785   0.317  "C2'"   OKT   4  
OKT  "C3'"   C5   C  0  1  N  N  R   9.328  -26.347  38.083   0.010  -2.293   0.167  "C3'"   OKT   5  
OKT  C4      C6   C  0  1  N  N  N  13.790  -25.047  35.236   4.499   2.106   0.072  C4      OKT   6  
OKT  "C4'"   C7   C  0  1  N  N  R   9.255  -27.809  37.641  -0.706  -1.167  -0.605  "C4'"   OKT   7  
OKT  C5      C8   C  0  1  N  N  N  12.692  -25.733  34.764   4.664   1.248  -1.042  C5      OKT   8  
OKT  "C5'"   C9   C  0  1  N  N  N   8.382  -27.943  36.557  -1.886  -0.642   0.215  "C5'"   OKT   9  
OKT  C6      C10  C  0  1  N  N  N  11.935  -26.472  35.654   3.706   0.338  -1.318  C6      OKT  10  
OKT  N1      N1   N  0  1  N  N  N  12.291  -26.493  36.923   2.599   0.256  -0.518  N1      OKT  11  
OKT  N3      N2   N  0  1  N  N  N  14.104  -25.103  36.523   3.394   1.993   0.836  N3      OKT  12  
OKT  O01     O1   O  0  1  N  N  N  10.380  -26.797  40.048   2.399  -2.846   0.106  O01     OKT  13  
OKT  O2      O2   O  0  1  N  N  N  13.666  -25.854  38.515   1.466   0.982   1.240  O2      OKT  14  
OKT  "O3'"   O3   O  0  1  N  N  N   8.213  -26.024  39.022  -0.021  -3.510  -0.580  "O3'"   OKT  15  
OKT  O4      O4   O  0  1  N  N  N  14.565  -24.298  34.360   5.348   2.938   0.338  O4      OKT  16  
OKT  "O4'"   O5   O  0  1  N  N  N  10.734  -28.127  37.218   0.253  -0.116  -0.814  "O4'"   OKT  17  
OKT  "O5'"   O6   O  0  1  N  N  N   9.127  -28.298  35.404  -2.612   0.317  -0.556  "O5'"   OKT  18  
OKT  OP1     O7   O  0  1  N  N  N   6.794  -27.598  34.103  -3.598   1.748   1.275  OP1     OKT  19  
OKT  P       P1   P  0  1  N  N  N   8.286  -28.310  33.906  -3.920   1.077  -0.004  P       OKT  20  
OKT  S01     S1   S  0  1  N  N  N   9.360  -27.355  32.477  -5.475  -0.330   0.308  S01     OKT  21  
OKT  H1      H1   H  0  1  N  N  N  11.322  -27.019  41.826   3.576  -4.246   1.066  H1      OKT  22  
OKT  H2      H2   H  0  1  N  N  N  12.353  -27.122  40.360   3.370  -2.700   1.924  H2      OKT  23  
OKT  H3      H3   H  0  1  N  N  N  11.712  -25.532  40.897   2.029  -3.869   1.863  H3      OKT  24  
OKT  H4      H4   H  0  1  N  N  N  12.156  -27.770  38.577   1.754  -1.215  -1.774  H4      OKT  25  
OKT  H5      H5   H  0  1  N  N  N  10.933  -25.280  38.701   1.617  -1.322   1.291  H5      OKT  26  
OKT  H6      H6   H  0  1  N  N  N   9.281  -25.692  37.201  -0.447  -2.436   1.147  H6      OKT  27  
OKT  H7      H7   H  0  1  N  N  N   8.967  -28.448  38.488  -1.059  -1.543  -1.565  H7      OKT  28  
OKT  H8      H8   H  0  1  N  N  N  12.428  -25.694  33.718   5.542   1.324  -1.666  H8      OKT  29  
OKT  H9      H9   H  0  1  N  N  N   7.863  -26.989  36.381  -2.544  -1.471   0.475  H9      OKT  30  
OKT  H10     H10  H  0  1  N  N  N   7.643  -28.728  36.774  -1.516  -0.172   1.125  H10     OKT  31  
OKT  H11     H11  H  0  1  N  N  N  11.069  -27.021  35.316   3.814  -0.325  -2.164  H11     OKT  32  
OKT  H12     H12  H  0  1  N  N  N  14.902  -24.604  36.862   3.274   2.578   1.601  H12     OKT  33  
OKT  H13     H13  H  0  1  N  N  N   8.274  -25.113  39.286  -0.909  -3.873  -0.705  H13     OKT  34  
OKT  H15     H15  H  0  1  N  N  N  10.466  -28.039  32.468  -5.659  -0.854  -0.917  H15     OKT  35  
OKT  OP3     O8   O  0  1  N  Y  N       ?        ?       ?  -4.397   2.175  -1.081  OP3     OKT  36  
OKT  HOP3    H16  H  0  0  N  Y  N       ?        ?       ?  -5.183   2.672  -0.814  HOP3    OKT  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
OKT  S01     P      SING  N  N   1  
OKT  P       OP1    DOUB  N  N   2  
OKT  P       "O5'"  SING  N  N   3  
OKT  O4      C4     DOUB  N  N   4  
OKT  C5      C4     SING  N  N   5  
OKT  C5      C6     DOUB  N  N   6  
OKT  C4      N3     SING  N  N   7  
OKT  "O5'"   "C5'"  SING  N  N   8  
OKT  C6      N1     SING  N  N   9  
OKT  N3      C2     SING  N  N  10  
OKT  "C5'"   "C4'"  SING  N  N  11  
OKT  N1      C2     SING  N  N  12  
OKT  N1      "C1'"  SING  N  N  13  
OKT  "O4'"   "C4'"  SING  N  N  14  
OKT  "O4'"   "C1'"  SING  N  N  15  
OKT  C2      O2     DOUB  N  N  16  
OKT  "C4'"   "C3'"  SING  N  N  17  
OKT  "C1'"   "C2'"  SING  N  N  18  
OKT  "C3'"   "C2'"  SING  N  N  19  
OKT  "C3'"   "O3'"  SING  N  N  20  
OKT  "C2'"   O01    SING  N  N  21  
OKT  O01     C02    SING  N  N  22  
OKT  C02     H1     SING  N  N  23  
OKT  C02     H2     SING  N  N  24  
OKT  C02     H3     SING  N  N  25  
OKT  "C1'"   H4     SING  N  N  26  
OKT  "C2'"   H5     SING  N  N  27  
OKT  "C3'"   H6     SING  N  N  28  
OKT  "C4'"   H7     SING  N  N  29  
OKT  C5      H8     SING  N  N  30  
OKT  "C5'"   H9     SING  N  N  31  
OKT  "C5'"   H10    SING  N  N  32  
OKT  C6      H11    SING  N  N  33  
OKT  N3      H12    SING  N  N  34  
OKT  "O3'"   H13    SING  N  N  35  
OKT  S01     H15    SING  N  N  36  
OKT  OP3     P      SING  N  N  37  
OKT  HOP3    OP3    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
OKT  InChI             InChI                 1.03   "InChI=1S/C10H15N2O8PS/c1-18-8-7(14)5(4-19-21(16,17)22)20-9(8)12-3-2-6(13)11-10(12)15/h2-3,5,7-9,14H,4H2,1H3,(H,11,13,15)(H2,16,17,22)/t5-,7-,8-,9-/m1/s1"  
OKT  InChIKey          InChI                 1.03   IEWLRLDHDVZUFQ-ZOQUXTDFSA-N  
OKT  SMILES_CANONICAL  CACTVS                3.385  "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(S)=O)O[C@H]1N2C=CC(=O)NC2=O"  
OKT  SMILES            CACTVS                3.385  "CO[CH]1[CH](O)[CH](CO[P](O)(S)=O)O[CH]1N2C=CC(=O)NC2=O"  
OKT  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)S)O"  
OKT  SMILES            "OpenEye OEToolkits"  2.0.7  "COC1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)S)O"  
#
_pdbx_chem_comp_identifier.comp_id          OKT
_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~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-methoxy-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
OKT  "Create component"  2020-03-19  PDBE  
OKT  "Initial release"   2020-04-29  RCSB  
##
