data_K39 # _chem_comp.id K39 _chem_comp.name "2'-methoxyethyl-guanosine-5'-thiophosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H20 N5 O8 P S" _chem_comp.mon_nstd_parent_comp_id DG _chem_comp.pdbx_synonyms "2-azanyl-9-[(2R,3R,4R,5R)-5-[bis(oxidanyl)phosphinothioyloxymethyl]-3-(2-methoxyethoxy)-4-oxidanyl-oxolan-2-yl]-1H-purin-6-one" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-05-17 _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 437.365 _chem_comp.one_letter_code G _chem_comp.three_letter_code K39 _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 K39 "C1'" C1 C 0 1 N N R -10.130 -21.968 -24.872 -0.285 -0.024 0.610 "C1'" K39 1 K39 C2 C2 C 0 1 N N N -9.309 -21.022 -20.723 -4.648 0.950 0.870 C2 K39 2 K39 "C2'" C3 C 0 1 N N R -11.623 -22.275 -24.748 -0.318 -1.216 -0.380 "C2'" K39 3 K39 "C3'" C4 C 0 1 N N R -12.171 -21.705 -26.042 0.999 -1.956 -0.041 "C3'" K39 4 K39 C4 C5 C 0 1 Y N N -9.514 -20.535 -22.875 -2.438 1.255 0.269 C4 K39 5 K39 "C4'" C6 C 0 1 N N R -11.056 -22.029 -27.030 1.863 -0.888 0.658 "C4'" K39 6 K39 C5 C7 C 0 1 Y N N -9.145 -19.214 -22.736 -2.766 2.451 -0.379 C5 K39 7 K39 "C5'" C8 C 0 1 N N N -10.993 -21.160 -28.261 3.174 -0.697 -0.109 "C5'" K39 8 K39 C6 C9 C 0 1 N N N -8.802 -18.733 -21.444 -4.114 2.879 -0.371 C6 K39 9 K39 C8 C10 C 0 1 Y N N -9.523 -19.490 -24.813 -0.631 2.158 -0.612 C8 K39 10 K39 "CA'" C11 C 0 1 N N N -11.308 -24.270 -23.449 -1.948 -2.715 -1.298 "CA'" K39 11 K39 "CB'" C12 C 0 1 N N N -11.065 -25.730 -23.660 -3.153 -3.577 -0.918 "CB'" K39 12 K39 "CD'" C13 C 0 1 N N N -10.308 -27.104 -25.411 -5.400 -3.446 -0.095 "CD'" K39 13 K39 N1 N1 N 0 1 N N N -8.915 -19.730 -20.481 -5.028 2.106 0.256 N1 K39 14 K39 N2 N2 N 0 1 N N N -9.347 -21.839 -19.659 -5.599 0.185 1.498 N2 K39 15 K39 N3 N3 N 0 1 N N N -9.628 -21.484 -21.921 -3.398 0.544 0.873 N3 K39 16 K39 N7 N4 N 0 1 Y N N -9.164 -18.565 -23.964 -1.619 2.955 -0.897 N7 K39 17 K39 N9 N5 N 0 1 Y N N -9.744 -20.711 -24.219 -1.090 1.090 0.103 N9 K39 18 K39 "O2'" O1 O 0 1 N N N -11.803 -23.687 -24.658 -1.450 -2.053 -0.133 "O2'" K39 19 K39 "O3'" O2 O 0 1 N N N -13.395 -22.342 -26.412 0.745 -3.052 0.841 "O3'" K39 20 K39 "O4'" O3 O 0 1 N N N -9.842 -21.864 -26.266 1.112 0.338 0.655 "O4'" K39 21 K39 "O5'" O4 O 0 1 N N N -11.091 -19.780 -27.878 4.010 0.221 0.599 "O5'" K39 22 K39 O6 O5 O 0 1 N N N -8.422 -17.602 -21.118 -4.444 3.915 -0.923 O6 K39 23 K39 "OC'" O6 O 0 1 N N N -11.139 -26.019 -25.037 -4.220 -2.736 -0.476 "OC'" K39 24 K39 OP2 O7 O 0 1 N Y N -11.750 -18.710 -30.043 6.276 1.367 1.278 OP2 K39 25 K39 P P1 P 0 1 N N N -10.783 -18.613 -28.918 5.470 0.656 0.080 P K39 26 K39 SP1 S8 S 0 1 N N N -10.773 -17.048 -27.840 6.404 -0.854 -0.487 SP1 K39 27 K39 "H1'" H1 H 0 1 N N N -9.562 -22.800 -24.431 -0.636 -0.333 1.595 "H1'" K39 28 K39 "H2'" H2 H 0 1 N N N -12.052 -21.750 -23.882 -0.313 -0.865 -1.412 "H2'" K39 29 K39 "H3'" H3 H 0 1 N N N -12.294 -20.615 -25.955 1.486 -2.305 -0.951 "H3'" K39 30 K39 "H4'" H4 H 0 1 N N N -11.158 -23.079 -27.342 2.073 -1.193 1.683 "H4'" K39 31 K39 "H5'" H5 H 0 1 N N N -11.826 -21.414 -28.932 3.684 -1.656 -0.202 "H5'" K39 32 K39 "H5''" H6 H 0 0 N N N -10.039 -21.329 -28.781 2.960 -0.301 -1.102 "H5''" K39 33 K39 H8 H7 H 0 1 N N N -9.635 -19.314 -25.873 0.398 2.317 -0.899 H8 K39 34 K39 H2 H8 H 0 1 N N N -10.365 -23.779 -23.165 -1.166 -3.347 -1.718 H2 K39 35 K39 H9 H9 H 0 1 N N N -12.048 -24.134 -22.647 -2.251 -1.972 -2.036 H9 K39 36 K39 H10 H10 H 0 1 N N N -11.827 -26.311 -23.121 -3.478 -4.150 -1.786 H10 K39 37 K39 H11 H11 H 0 1 N N N -10.067 -25.995 -23.282 -2.873 -4.260 -0.116 H11 K39 38 K39 H12 H12 H 0 1 N N N -10.405 -27.285 -26.492 -6.163 -2.737 0.228 H12 K39 39 K39 H13 H13 H 0 1 N N N -9.262 -26.864 -25.172 -5.772 -4.017 -0.946 H13 K39 40 K39 H14 H14 H 0 1 N N N -10.612 -28.006 -24.860 -5.167 -4.127 0.724 H14 K39 41 K39 H1 H15 H 0 1 N N N -8.691 -19.486 -19.537 -5.960 2.375 0.268 H1 K39 42 K39 H21 H16 H 0 1 N N N -9.616 -22.795 -19.772 -6.526 0.470 1.500 H21 K39 43 K39 H22 H17 H 0 1 N N N -9.106 -21.491 -18.753 -5.343 -0.640 1.939 H22 K39 44 K39 "HO3'" H18 H 0 0 N Y N -14.070 -22.123 -25.780 1.536 -3.551 1.086 "HO3'" K39 45 K39 HOP2 H19 H 0 0 N Y N -12.275 -17.919 -30.079 7.167 1.657 1.036 HOP2 K39 46 K39 OP3 O9 O 0 1 N N N -9.302 -18.957 -29.432 5.318 1.686 -1.149 OP3 K39 47 K39 HOP3 H20 H 0 0 N N N -8.692 -18.309 -29.099 4.841 2.497 -0.926 HOP3 K39 48 # 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 K39 OP2 P SING N N 1 K39 P "O5'" SING N N 2 K39 P SP1 DOUB N N 3 K39 "C5'" "O5'" SING N N 4 K39 "C5'" "C4'" SING N N 5 K39 "C4'" "O4'" SING N N 6 K39 "C4'" "C3'" SING N N 7 K39 "O3'" "C3'" SING N N 8 K39 "O4'" "C1'" SING N N 9 K39 "C3'" "C2'" SING N N 10 K39 "CD'" "OC'" SING N N 11 K39 "OC'" "CB'" SING N N 12 K39 "C1'" "C2'" SING N N 13 K39 "C1'" N9 SING N N 14 K39 C8 N9 SING Y N 15 K39 C8 N7 DOUB Y N 16 K39 "C2'" "O2'" SING N N 17 K39 "O2'" "CA'" SING N N 18 K39 N9 C4 SING Y N 19 K39 N7 C5 SING Y N 20 K39 "CB'" "CA'" SING N N 21 K39 C4 C5 DOUB Y N 22 K39 C4 N3 SING N N 23 K39 C5 C6 SING N N 24 K39 N3 C2 DOUB N N 25 K39 C6 O6 DOUB N N 26 K39 C6 N1 SING N N 27 K39 C2 N1 SING N N 28 K39 C2 N2 SING N N 29 K39 "C1'" "H1'" SING N N 30 K39 "C2'" "H2'" SING N N 31 K39 "C3'" "H3'" SING N N 32 K39 "C4'" "H4'" SING N N 33 K39 "C5'" "H5'" SING N N 34 K39 "C5'" "H5''" SING N N 35 K39 C8 H8 SING N N 36 K39 "CA'" H2 SING N N 37 K39 "CA'" H9 SING N N 38 K39 "CB'" H10 SING N N 39 K39 "CB'" H11 SING N N 40 K39 "CD'" H12 SING N N 41 K39 "CD'" H13 SING N N 42 K39 "CD'" H14 SING N N 43 K39 N1 H1 SING N N 44 K39 N2 H21 SING N N 45 K39 N2 H22 SING N N 46 K39 "O3'" "HO3'" SING N N 47 K39 OP2 HOP2 SING N N 48 K39 P OP3 SING N N 49 K39 OP3 HOP3 SING N N 50 # 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 K39 InChI InChI 1.06 "InChI=1S/C13H20N5O8PS/c1-23-2-3-24-9-8(19)6(4-25-27(21,22)28)26-12(9)18-5-15-7-10(18)16-13(14)17-11(7)20/h5-6,8-9,12,19H,2-4H2,1H3,(H2,21,22,28)(H3,14,16,17,20)/t6-,8-,9-,12-/m1/s1" K39 InChIKey InChI 1.06 QOLXKMFPGMBQJQ-WOUKDFQISA-N K39 SMILES_CANONICAL CACTVS 3.385 "COCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=S)O[C@H]1n2cnc3C(=O)NC(=Nc23)N" K39 SMILES CACTVS 3.385 "COCCO[CH]1[CH](O)[CH](CO[P](O)(O)=S)O[CH]1n2cnc3C(=O)NC(=Nc23)N" K39 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COCCO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2N=C(NC3=O)N)COP(=S)(O)O)O" K39 SMILES "OpenEye OEToolkits" 2.0.7 "COCCOC1C(C(OC1n2cnc3c2N=C(NC3=O)N)COP(=S)(O)O)O" # _pdbx_chem_comp_identifier.comp_id K39 _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-azanyl-9-[(2~{R},3~{R},4~{R},5~{R})-5-[bis(oxidanyl)phosphinothioyloxymethyl]-3-(2-methoxyethoxy)-4-oxidanyl-oxolan-2-yl]-1~{H}-purin-6-one" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id K39 _pdbx_chem_comp_synonyms.name "2-azanyl-9-[(2R,3R,4R,5R)-5-[bis(oxidanyl)phosphinothioyloxymethyl]-3-(2-methoxyethoxy)-4-oxidanyl-oxolan-2-yl]-1H-purin-6-one" _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 K39 "Create component" 2022-05-17 PDBE K39 "Modify linking type" 2022-06-15 PDBE K39 "Modify descriptor" 2022-08-22 RCSB K39 "Initial release" 2022-09-14 RCSB #