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 ##