data_K2F # _chem_comp.id K2F _chem_comp.name "2'-methoxyethyl-adenosine-5'-thiophosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H20 N5 O7 P S" _chem_comp.mon_nstd_parent_comp_id DA _chem_comp.pdbx_synonyms "(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-2-[bis(oxidanyl)phosphinothioyloxymethyl]-4-(2-methoxyethoxy)oxolan-3-ol" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-05-16 _chem_comp.pdbx_modified_date 2022-09-09 _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 421.366 _chem_comp.one_letter_code A _chem_comp.three_letter_code K2F _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 7ZVN _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 K2F C2 C1 C 0 1 Y N N -15.160 -10.411 -14.184 4.779 -1.069 1.030 C2 K2F 1 K2F C4 C2 C 0 1 Y N N -14.570 -8.571 -15.235 2.567 -1.271 0.441 C4 K2F 2 K2F "C1'" C3 C 0 1 N N R -14.037 -6.216 -14.486 0.456 0.098 0.717 "C1'" K2F 3 K2F "C2'" C4 C 0 1 N N R -12.712 -6.287 -13.710 0.547 1.252 -0.313 "C2'" K2F 4 K2F "C3'" C5 C 0 1 N N R -11.849 -5.322 -14.498 -0.742 2.056 -0.014 "C3'" K2F 5 K2F "C4'" C6 C 0 1 N N R -12.852 -4.224 -14.821 -1.655 1.049 0.712 "C4'" K2F 6 K2F C5 C7 C 0 1 Y N N -14.647 -9.185 -16.471 2.852 -2.508 -0.162 C5 K2F 7 K2F "C5'" C8 C 0 1 N N N -12.475 -3.267 -15.927 -2.967 0.886 -0.059 "C5'" K2F 8 K2F C6 C9 C 0 1 Y N N -15.039 -10.536 -16.490 4.175 -2.979 -0.116 C6 K2F 9 K2F C8 C10 C 0 1 Y N N -14.059 -7.178 -16.847 0.732 -2.136 -0.423 C8 K2F 10 K2F "CA'" C11 C 0 1 N N N -12.655 -6.657 -11.336 2.245 2.649 -1.267 "CA'" K2F 11 K2F "CB'" C12 C 0 1 N N N -13.894 -7.429 -11.027 3.481 3.476 -0.905 "CB'" K2F 12 K2F "CD'" C13 C 0 1 N N N -14.652 -9.612 -10.547 5.713 3.283 -0.054 "CD'" K2F 13 K2F N1 N1 N 0 1 Y N N -15.292 -11.133 -15.304 5.095 -2.228 0.482 N1 K2F 14 K2F N3 N2 N 0 1 Y N N -14.812 -9.135 -14.038 3.552 -0.592 1.019 N3 K2F 15 K2F N6 N3 N 0 1 N N N -15.197 -11.246 -17.610 4.516 -4.191 -0.691 N6 K2F 16 K2F N7 N4 N 0 1 Y N N -14.315 -8.295 -17.483 1.689 -2.983 -0.669 N7 K2F 17 K2F N9 N5 N 0 1 Y N N -14.202 -7.270 -15.484 1.223 -1.064 0.260 N9 K2F 18 K2F "O2'" O1 O 0 1 N N N -12.912 -5.748 -12.406 1.710 2.050 -0.085 "O2'" K2F 19 K2F "O3'" O2 O 0 1 N N N -10.741 -4.831 -13.742 -0.452 3.169 0.833 "O3'" K2F 20 K2F "O4'" O3 O 0 1 N N N -14.060 -4.947 -15.149 -0.955 -0.205 0.761 "O4'" K2F 21 K2F "O5'" O4 O 0 1 N N N -12.469 -3.920 -17.204 -3.852 0.043 0.680 "O5'" K2F 22 K2F "OC'" O5 O 0 1 N N N -13.559 -8.704 -10.512 4.509 2.608 -0.422 "OC'" K2F 23 K2F OP2 O6 O 0 1 N Y N -11.246 -2.062 -18.315 -6.311 0.915 0.354 OP2 K2F 24 K2F P P1 P 0 1 N N N -12.299 -3.082 -18.547 -5.327 -0.346 0.165 P K2F 25 K2F SP1 SP1 S 0 1 N N N -12.035 -4.392 -19.900 -5.254 -0.811 -1.638 SP1 K2F 26 K2F "H1'" H1 H 0 1 N N N -15.366 -10.941 -13.266 5.557 -0.492 1.509 "H1'" K2F 27 K2F H1 H2 H 0 1 N N N -14.863 -6.270 -13.762 0.808 0.428 1.695 H1 K2F 28 K2F "H2'" H3 H 0 1 N N N -12.296 -7.305 -13.706 0.537 0.865 -1.332 "H2'" K2F 29 K2F "H3'" H4 H 0 1 N N N -11.511 -5.800 -15.429 -1.205 2.394 -0.942 "H3'" K2F 30 K2F "H4'" H5 H 0 1 N N N -13.022 -3.639 -13.905 -1.861 1.398 1.724 "H4'" K2F 31 K2F "H5'" H6 H 0 1 N N N -11.471 -2.865 -15.726 -3.429 1.863 -0.200 "H5'" K2F 32 K2F "H5''" H7 H 0 0 N N N -13.202 -2.442 -15.950 -2.764 0.437 -1.031 "H5''" K2F 33 K2F H8 H8 H 0 1 N N N -13.763 -6.269 -17.349 -0.299 -2.265 -0.716 H8 K2F 34 K2F H9 H9 H 0 1 N N N -11.854 -7.352 -11.630 1.493 3.298 -1.717 H9 K2F 35 K2F H10 H10 H 0 1 N N N -12.343 -6.094 -10.444 2.524 1.870 -1.975 H10 K2F 36 K2F H11 H11 H 0 1 N N N -14.488 -6.880 -10.281 3.836 4.004 -1.789 H11 K2F 37 K2F H12 H12 H 0 1 N N N -14.484 -7.552 -11.947 3.221 4.197 -0.130 H12 K2F 38 K2F H13 H13 H 0 1 N N N -14.336 -10.583 -10.137 6.115 3.807 -0.921 H13 K2F 39 K2F H14 H14 H 0 1 N N N -15.481 -9.211 -9.945 5.500 4.001 0.738 H14 K2F 40 K2F H15 H15 H 0 1 N N N -14.985 -9.745 -11.587 6.443 2.556 0.301 H15 K2F 41 K2F H61 H16 H 0 1 N N N -15.498 -12.171 -17.379 3.838 -4.726 -1.133 H61 K2F 42 K2F H62 H17 H 0 1 N N N -15.884 -10.807 -18.189 5.433 -4.505 -0.652 H62 K2F 43 K2F "HO3'" H18 H 0 0 N Y N -10.140 -5.544 -13.561 -1.224 3.708 1.053 "HO3'" K2F 44 K2F HOP2 H19 H 0 0 N Y N -10.525 -2.208 -18.917 -6.397 1.212 1.271 HOP2 K2F 45 K2F OP3 O8 O 0 1 N N N -13.728 -2.369 -18.722 -5.883 -1.592 1.019 OP3 K2F 46 K2F HOP3 H20 H 0 0 N N N -14.177 -2.738 -19.474 -6.769 -1.881 0.762 HOP3 K2F 47 # 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 K2F SP1 P DOUB N N 1 K2F P OP2 SING N N 2 K2F P "O5'" SING N N 3 K2F N6 C6 SING N N 4 K2F N7 C8 DOUB Y N 5 K2F N7 C5 SING Y N 6 K2F "O5'" "C5'" SING N N 7 K2F C8 N9 SING Y N 8 K2F C6 C5 DOUB Y N 9 K2F C6 N1 SING Y N 10 K2F C5 C4 SING Y N 11 K2F "C5'" "C4'" SING N N 12 K2F N9 C4 SING Y N 13 K2F N9 "C1'" SING N N 14 K2F N1 C2 DOUB Y N 15 K2F C4 N3 DOUB Y N 16 K2F "O4'" "C4'" SING N N 17 K2F "O4'" "C1'" SING N N 18 K2F "C4'" "C3'" SING N N 19 K2F "C3'" "O3'" SING N N 20 K2F "C3'" "C2'" SING N N 21 K2F "C1'" "C2'" SING N N 22 K2F C2 N3 SING Y N 23 K2F "C2'" "O2'" SING N N 24 K2F "O2'" "CA'" SING N N 25 K2F "CA'" "CB'" SING N N 26 K2F "CB'" "OC'" SING N N 27 K2F "CD'" "OC'" SING N N 28 K2F C2 "H1'" SING N N 29 K2F "C1'" H1 SING N N 30 K2F "C2'" "H2'" SING N N 31 K2F "C3'" "H3'" SING N N 32 K2F "C4'" "H4'" SING N N 33 K2F "C5'" "H5'" SING N N 34 K2F "C5'" "H5''" SING N N 35 K2F C8 H8 SING N N 36 K2F "CA'" H9 SING N N 37 K2F "CA'" H10 SING N N 38 K2F "CB'" H11 SING N N 39 K2F "CB'" H12 SING N N 40 K2F "CD'" H13 SING N N 41 K2F "CD'" H14 SING N N 42 K2F "CD'" H15 SING N N 43 K2F N6 H61 SING N N 44 K2F N6 H62 SING N N 45 K2F "O3'" "HO3'" SING N N 46 K2F OP2 HOP2 SING N N 47 K2F P OP3 SING N N 48 K2F OP3 HOP3 SING N N 49 # 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 K2F InChI InChI 1.06 "InChI=1S/C13H20N5O7PS/c1-22-2-3-23-10-9(19)7(4-24-26(20,21)27)25-13(10)18-6-17-8-11(14)15-5-16-12(8)18/h5-7,9-10,13,19H,2-4H2,1H3,(H2,14,15,16)(H2,20,21,27)/t7-,9-,10-,13-/m1/s1" K2F InChIKey InChI 1.06 ZQSIUNNJVQJWJZ-QYVSTXNMSA-N K2F SMILES_CANONICAL CACTVS 3.385 "COCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=S)O[C@H]1n2cnc3c(N)ncnc23" K2F SMILES CACTVS 3.385 "COCCO[CH]1[CH](O)[CH](CO[P](O)(O)=S)O[CH]1n2cnc3c(N)ncnc23" K2F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COCCO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2ncnc3N)COP(=S)(O)O)O" K2F SMILES "OpenEye OEToolkits" 2.0.7 "COCCOC1C(C(OC1n2cnc3c2ncnc3N)COP(=S)(O)O)O" # _pdbx_chem_comp_identifier.comp_id K2F _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-(6-aminopurin-9-yl)-2-[bis(oxidanyl)phosphinothioyloxymethyl]-4-(2-methoxyethoxy)oxolan-3-ol" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id K2F _pdbx_chem_comp_synonyms.name "(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-2-[bis(oxidanyl)phosphinothioyloxymethyl]-4-(2-methoxyethoxy)oxolan-3-ol" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site K2F "Create component" 2022-05-16 PDBE K2F "Modify linking type" 2022-06-15 PDBE K2F "Modify descriptor" 2022-08-22 RCSB K2F "Initial release" 2022-09-14 RCSB #