data_ILK # _chem_comp.id ILK _chem_comp.name "[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)selenolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H13 N2 O8 P Se" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-07-07 _chem_comp.pdbx_modified_date 2023-04-28 _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 387.142 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ILK _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 7Y8P _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 ILK "C1'" C1 C 0 1 N N R 1.752 2.247 26.857 1.377 1.048 0.175 "C1'" ILK 1 ILK C2 C2 C 0 1 N N N -0.617 2.499 27.592 3.638 0.263 -0.252 C2 ILK 2 ILK "C2'" C3 C 0 1 N N R 2.721 2.548 28.011 0.477 1.168 -1.090 "C2'" ILK 3 ILK "C3'" C4 C 0 1 N N S 3.436 1.252 28.509 -0.813 1.918 -0.786 "C3'" ILK 4 ILK C4 C5 C 0 1 N N N -2.044 0.650 28.121 4.207 -2.003 -0.239 C4 ILK 5 ILK "C4'" C6 C 0 1 N N R 4.058 0.598 27.276 -1.376 1.722 0.634 "C4'" ILK 6 ILK C5 C7 C 0 1 N N N -0.948 -0.290 27.885 2.862 -2.328 0.062 C5 ILK 7 ILK "C5'" C8 C 0 1 N N N 4.407 -0.866 27.516 -2.721 0.994 0.584 "C5'" ILK 8 ILK C6 C9 C 0 1 N N N 0.274 0.262 27.511 1.959 -1.332 0.192 C6 ILK 9 ILK N1 N1 N 0 1 N N N 0.504 1.620 27.311 2.356 -0.032 0.033 N1 ILK 10 ILK N3 N2 N 0 1 N N N -1.881 1.956 27.971 4.558 -0.710 -0.387 N3 ILK 11 ILK O2 O1 O 0 1 N N N -0.387 3.710 27.432 3.968 1.424 -0.393 O2 ILK 12 ILK "O2'" O2 O 0 1 N N N 3.676 3.487 27.552 1.195 1.866 -2.109 "O2'" ILK 13 ILK "O3'" O3 O 0 1 N N N 4.411 1.683 29.455 -0.577 3.313 -0.985 "O3'" ILK 14 ILK O4 O4 O 0 1 N N N -3.282 0.135 28.501 5.039 -2.884 -0.361 O4 ILK 15 ILK "O5'" O5 O 0 1 N N N 3.256 -1.502 27.931 -2.571 -0.235 -0.130 "O5'" ILK 16 ILK OP1 O6 O 0 1 N N N 4.227 -3.573 29.076 -4.401 -1.620 0.921 OP1 ILK 17 ILK OP2 O7 O 0 1 N N N 1.694 -3.427 28.755 -4.894 -0.563 -1.317 OP2 ILK 18 ILK P P1 P 0 1 N N N 3.067 -3.198 28.236 -3.788 -1.260 -0.377 P ILK 19 ILK SE4 SE1 SE 0 0 N N N 2.766 0.903 25.891 -0.009 0.598 1.530 SE4 ILK 20 ILK H1 H1 H 0 1 N N N 1.604 3.107 26.187 1.866 1.995 0.405 H1 ILK 21 ILK H2 H2 H 0 1 N N N 2.147 2.969 28.850 0.233 0.168 -1.449 H2 ILK 22 ILK H3 H3 H 0 1 N N N 2.699 0.575 28.966 -1.571 1.597 -1.500 H3 ILK 23 ILK H4 H4 H 0 1 N N N 4.958 1.153 26.972 -1.480 2.681 1.141 H4 ILK 24 ILK H5 H5 H 0 1 N N N -1.080 -1.356 27.995 2.562 -3.358 0.185 H5 ILK 25 ILK H6 H6 H 0 1 N N N 4.774 -1.323 26.585 -3.060 0.786 1.598 H6 ILK 26 ILK H7 H7 H 0 1 N N N 5.181 -0.945 28.293 -3.455 1.621 0.077 H7 ILK 27 ILK H8 H8 H 0 1 N N N 1.104 -0.413 27.365 0.929 -1.560 0.421 H8 ILK 28 ILK H9 H9 H 0 1 N N N -2.655 2.570 28.126 5.477 -0.480 -0.593 H9 ILK 29 ILK H10 H10 H 0 1 N N N 4.286 3.687 28.252 0.698 1.980 -2.931 H10 ILK 30 ILK H11 H11 H 0 1 N N N 3.976 2.081 30.200 -0.328 3.545 -1.890 H11 ILK 31 ILK H13 H13 H 0 1 N N N 1.743 -3.813 29.622 -4.562 -0.300 -2.186 H13 ILK 32 ILK OP3 OP3 O 0 1 N N N 3.357 -3.954 26.905 -3.233 -2.589 -1.095 OP3 ILK 33 ILK H12 H12 H 0 1 N N N 4.172 -4.436 26.985 -3.914 -3.253 -1.275 H12 ILK 34 # 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 ILK SE4 "C1'" SING N N 1 ILK SE4 "C4'" SING N N 2 ILK "C1'" N1 SING N N 3 ILK "C1'" "C2'" SING N N 4 ILK "C4'" "C5'" SING N N 5 ILK "C4'" "C3'" SING N N 6 ILK N1 C6 SING N N 7 ILK N1 C2 SING N N 8 ILK O2 C2 DOUB N N 9 ILK C6 C5 DOUB N N 10 ILK "C5'" "O5'" SING N N 11 ILK "O2'" "C2'" SING N N 12 ILK C2 N3 SING N N 13 ILK C5 C4 SING N N 14 ILK "O5'" P SING N N 15 ILK N3 C4 SING N N 16 ILK "C2'" "C3'" SING N N 17 ILK C4 O4 DOUB N N 18 ILK P OP2 SING N N 19 ILK P OP1 DOUB N N 20 ILK "C3'" "O3'" SING N N 21 ILK "C1'" H1 SING N N 22 ILK "C2'" H2 SING N N 23 ILK "C3'" H3 SING N N 24 ILK "C4'" H4 SING N N 25 ILK C5 H5 SING N N 26 ILK "C5'" H6 SING N N 27 ILK "C5'" H7 SING N N 28 ILK C6 H8 SING N N 29 ILK N3 H9 SING N N 30 ILK "O2'" H10 SING N N 31 ILK "O3'" H11 SING N N 32 ILK OP2 H13 SING N N 33 ILK P OP3 SING N N 34 ILK OP3 H12 SING N N 35 # 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 ILK InChI InChI 1.06 "InChI=1S/C9H13N2O8PSe/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(21-8)3-19-20(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1" ILK InChIKey InChI 1.06 QLPCUUUELDONBL-XVFCMESISA-N ILK SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H]([Se][C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O" ILK SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH]([Se][CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O" ILK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H]([Se]2)COP(=O)(O)O)O)O" ILK SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)C2C(C(C([Se]2)COP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id ILK _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},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)selenolan-2-yl]methyl dihydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site ILK "Create component" 2022-07-07 PDBJ ILK "Initial release" 2023-05-03 RCSB #