data_OKQ # _chem_comp.id OKQ _chem_comp.name "2'-O-methylcytidine-5'-phosphorothioate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N3 O7 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 353.289 _chem_comp.one_letter_code C _chem_comp.three_letter_code OKQ _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 OKQ C2 C1 C 0 1 N N N 8.316 -34.825 34.780 -2.235 -1.139 0.447 C2 OKQ 1 OKQ C4 C2 C 0 1 N N N 9.454 -36.701 34.090 -4.139 -2.341 -0.071 C4 OKQ 2 OKQ C5 C3 C 0 1 N N N 10.143 -35.948 33.168 -4.407 -1.454 -1.134 C5 OKQ 3 OKQ C6 C4 C 0 1 N N N 9.881 -34.601 33.087 -3.549 -0.433 -1.368 C6 OKQ 4 OKQ O2 O1 O 0 1 N N N 7.515 -34.312 35.483 -1.253 -0.989 1.154 O2 OKQ 5 OKQ "C1'" C5 C 0 1 N N R 8.655 -32.648 33.852 -1.532 0.830 -0.798 "C1'" OKQ 6 OKQ "C2'" C6 C 0 1 N N R 9.869 -31.725 33.787 -1.508 1.789 0.419 "C2'" OKQ 7 OKQ "C3'" C7 C 0 1 N N R 9.243 -30.489 33.166 -0.113 2.447 0.286 "C3'" OKQ 8 OKQ "C4'" C8 C 0 1 N N R 8.317 -31.105 32.122 0.685 1.465 -0.592 "C4'" OKQ 9 OKQ "C5'" C9 C 0 1 N N N 8.937 -31.330 30.762 1.932 0.988 0.155 "C5'" OKQ 10 OKQ CM2 C10 C 0 1 N N N 11.596 -30.722 35.037 -3.042 3.221 1.579 CM2 OKQ 11 OKQ N1 N1 N 0 1 N N N 8.976 -34.082 33.897 -2.461 -0.278 -0.563 N1 OKQ 12 OKQ N3 N2 N 0 1 N N N 8.560 -36.129 34.874 -3.063 -2.155 0.683 N3 OKQ 13 OKQ N4 N3 N 0 1 N N N 9.713 -38.123 34.202 -4.987 -3.394 0.182 N4 OKQ 14 OKQ "O2'" O2 O 0 1 N N N 10.447 -31.517 35.059 -2.546 2.767 0.318 "O2'" OKQ 15 OKQ "O3'" O3 O 0 1 N N N 8.451 -29.837 34.157 -0.220 3.720 -0.355 "O3'" OKQ 16 OKQ "O4'" O4 O 0 1 N N N 7.915 -32.390 32.671 -0.174 0.347 -0.877 "O4'" OKQ 17 OKQ "O5'" O5 O 0 1 N N N 8.246 -32.335 30.020 2.717 0.161 -0.707 "O5'" OKQ 18 OKQ H1 H1 H 0 1 N N N 10.876 -36.406 32.520 -5.278 -1.592 -1.757 H1 OKQ 19 OKQ H2 H2 H 0 1 N N N 10.405 -33.980 32.375 -3.733 0.260 -2.176 H2 OKQ 20 OKQ H3 H3 H 0 1 N N N 8.059 -32.381 34.737 -1.801 1.369 -1.706 H3 OKQ 21 OKQ H4 H4 H 0 1 N N N 10.606 -32.148 33.089 -1.590 1.234 1.354 H4 OKQ 22 OKQ H5 H5 H 0 1 N N N 9.997 -29.833 32.707 0.354 2.553 1.265 H5 OKQ 23 OKQ H6 H6 H 0 1 N N N 7.434 -30.459 32.008 0.974 1.957 -1.522 H6 OKQ 24 OKQ H7 H7 H 0 1 N N N 9.983 -31.643 30.896 2.521 1.850 0.467 H7 OKQ 25 OKQ H8 H8 H 0 1 N N N 8.906 -30.387 30.197 1.632 0.415 1.033 H8 OKQ 26 OKQ H9 H9 H 0 1 N N N 11.983 -30.608 36.060 -3.825 3.961 1.416 H9 OKQ 27 OKQ H10 H10 H 0 1 N N N 12.360 -31.200 34.407 -3.449 2.376 2.134 H10 OKQ 28 OKQ H11 H11 H 0 1 N N N 11.349 -29.732 34.626 -2.229 3.672 2.148 H11 OKQ 29 OKQ H12 H12 H 0 1 N N N 9.214 -38.671 34.874 -4.800 -4.002 0.914 H12 OKQ 30 OKQ H13 H13 H 0 1 N N N 10.391 -38.556 33.608 -5.773 -3.527 -0.371 H13 OKQ 31 OKQ H14 H14 H 0 1 N N N 9.019 -29.450 34.813 0.625 4.177 -0.465 H14 OKQ 32 OKQ P1 P1 P 0 1 N N N 7.331 -32.051 29.865 4.103 -0.517 -0.248 P1 OKQ 33 OKQ O1 O6 O 0 1 N N N ? ? ? 5.022 0.530 0.253 O1 OKQ 34 OKQ H17 H17 H 0 1 N N N ? ? ? 4.951 -2.402 1.572 H17 OKQ 35 OKQ S1 S1 S 0 1 N N N ? ? ? 3.726 -1.923 1.293 S1 OKQ 36 OKQ OP3 O7 O 0 1 N Y N ? ? ? 4.776 -1.265 -1.505 OP3 OKQ 37 OKQ HOP3 H18 H 0 0 N Y N ? ? ? 4.228 -1.965 -1.885 HOP3 OKQ 38 # # 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 OKQ "O5'" "C5'" SING N N 1 OKQ "C5'" "C4'" SING N N 2 OKQ "C4'" "O4'" SING N N 3 OKQ "C4'" "C3'" SING N N 4 OKQ "O4'" "C1'" SING N N 5 OKQ C6 C5 DOUB N N 6 OKQ C6 N1 SING N N 7 OKQ "C3'" "C2'" SING N N 8 OKQ "C3'" "O3'" SING N N 9 OKQ C5 C4 SING N N 10 OKQ "C2'" "C1'" SING N N 11 OKQ "C2'" "O2'" SING N N 12 OKQ "C1'" N1 SING N N 13 OKQ N1 C2 SING N N 14 OKQ C4 N4 SING N N 15 OKQ C4 N3 DOUB N N 16 OKQ C2 N3 SING N N 17 OKQ C2 O2 DOUB N N 18 OKQ CM2 "O2'" SING N N 19 OKQ C5 H1 SING N N 20 OKQ C6 H2 SING N N 21 OKQ "C1'" H3 SING N N 22 OKQ "C2'" H4 SING N N 23 OKQ "C3'" H5 SING N N 24 OKQ "C4'" H6 SING N N 25 OKQ "C5'" H7 SING N N 26 OKQ "C5'" H8 SING N N 27 OKQ CM2 H9 SING N N 28 OKQ CM2 H10 SING N N 29 OKQ CM2 H11 SING N N 30 OKQ N4 H12 SING N N 31 OKQ N4 H13 SING N N 32 OKQ "O3'" H14 SING N N 33 OKQ "O5'" P1 SING N N 34 OKQ O1 P1 DOUB N N 35 OKQ H17 S1 SING N N 36 OKQ S1 P1 SING N N 37 OKQ OP3 P1 SING N N 38 OKQ HOP3 OP3 SING N N 39 # # 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 OKQ InChI InChI 1.03 "InChI=1S/C10H16N3O7PS/c1-18-8-7(14)5(4-19-21(16,17)22)20-9(8)13-3-2-6(11)12-10(13)15/h2-3,5,7-9,14H,4H2,1H3,(H2,11,12,15)(H2,16,17,22)/t5-,7-,8-,9-/m1/s1" OKQ InChIKey InChI 1.03 JKIZWHJBBPPNBB-ZOQUXTDFSA-N OKQ SMILES_CANONICAL CACTVS 3.385 "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(S)=O)O[C@H]1N2C=CC(=NC2=O)N" OKQ SMILES CACTVS 3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(S)=O)O[CH]1N2C=CC(=NC2=O)N" OKQ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)S)O" OKQ SMILES "OpenEye OEToolkits" 2.0.7 "COC1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)S)O" # _pdbx_chem_comp_identifier.comp_id OKQ _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-(4-azanyl-2-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 OKQ "Create component" 2020-03-19 PDBE OKQ "Initial release" 2020-04-29 RCSB ##