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 ##