data_IKS # _chem_comp.id IKS _chem_comp.name "[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-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 H14 N3 O7 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 386.157 _chem_comp.one_letter_code ? _chem_comp.three_letter_code IKS _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 IKS P P1 P 0 1 N N N -0.005 -7.970 25.931 4.031 1.085 -0.416 P IKS 1 IKS OP1 O1 O 0 1 N N N 0.913 -9.032 26.379 5.070 0.235 -1.039 OP1 IKS 2 IKS OP2 O2 O 0 1 N N N -1.073 -7.503 26.835 3.686 2.316 -1.394 OP2 IKS 3 IKS "O5'" O3 O 0 1 N N N 0.985 -6.549 25.788 2.703 0.211 -0.164 "O5'" IKS 4 IKS "C5'" C1 C 0 1 N N N 2.311 -6.527 25.390 2.703 -1.010 0.579 "C5'" IKS 5 IKS "C4'" C2 C 0 1 N N R 2.603 -5.154 24.827 1.284 -1.579 0.626 "C4'" IKS 6 IKS "C3'" C3 C 0 1 N N S 2.336 -4.098 25.891 0.706 -1.749 -0.799 "C3'" IKS 7 IKS "O3'" O4 O 0 1 N N N 3.357 -3.954 26.905 0.927 -3.099 -1.213 "O3'" IKS 8 IKS "C2'" C4 C 0 1 N N R 2.146 -2.810 24.988 -0.771 -1.442 -0.948 "C2'" IKS 9 IKS "O2'" O5 O 0 1 N N N 3.468 -2.462 24.480 -1.422 -2.612 -1.449 "O2'" IKS 10 IKS "C1'" C5 C 0 1 N N R 1.138 -2.950 23.821 -1.497 -1.002 0.344 "C1'" IKS 11 IKS N1 N1 N 0 1 N N N -0.179 -2.898 24.424 -2.495 0.032 0.061 N1 IKS 12 IKS C2 C6 C 0 1 N N N -0.819 -1.593 24.390 -3.800 -0.292 0.010 C2 IKS 13 IKS O2 O6 O 0 1 N N N -0.179 -0.678 23.819 -4.138 -1.449 0.201 O2 IKS 14 IKS N3 N2 N 0 1 N N N -2.099 -1.324 24.961 -4.728 0.628 -0.244 N3 IKS 15 IKS C4 C7 C 0 1 N N N -2.794 -2.309 25.581 -4.388 1.893 -0.456 C4 IKS 16 IKS N4 N3 N 0 1 N N N -4.050 -2.097 26.142 -5.356 2.835 -0.718 N4 IKS 17 IKS C5 C8 C 0 1 N N N -2.164 -3.650 25.614 -3.029 2.266 -0.411 C5 IKS 18 IKS C6 C9 C 0 1 N N N -0.908 -3.889 25.076 -2.098 1.320 -0.145 C6 IKS 19 IKS SE4 SE1 SE 0 0 N N N 1.494 -4.767 23.268 0.013 -0.265 1.410 SE4 IKS 20 IKS H2 H2 H 0 1 N N N -1.029 -7.984 27.653 4.442 2.886 -1.590 H2 IKS 21 IKS H3 H3 H 0 1 N N N 2.483 -7.292 24.618 3.367 -1.728 0.097 H3 IKS 22 IKS H4 H4 H 0 1 N N N 2.964 -6.724 26.253 3.051 -0.818 1.594 H4 IKS 23 IKS H5 H5 H 0 1 N N N 3.644 -5.093 24.477 1.260 -2.522 1.173 H5 IKS 24 IKS H6 H6 H 0 1 N N N 1.370 -4.319 26.369 1.260 -1.094 -1.472 H6 IKS 25 IKS H7 H7 H 0 1 N N N 3.101 -3.276 27.519 0.595 -3.298 -2.099 H7 IKS 26 IKS H8 H8 H 0 1 N N N 1.791 -2.000 25.642 -0.882 -0.650 -1.689 H8 IKS 27 IKS H9 H9 H 0 1 N N N 4.075 -2.380 25.206 -1.108 -2.895 -2.319 H9 IKS 28 IKS H10 H10 H 0 1 N N N 1.317 -2.268 22.977 -1.953 -1.855 0.847 H10 IKS 29 IKS H11 H11 H 0 1 N N N -4.472 -1.191 26.096 -6.290 2.575 -0.748 H11 IKS 30 IKS H12 H12 H 0 1 N N N -4.531 -2.850 26.591 -5.104 3.759 -0.872 H12 IKS 31 IKS H13 H13 H 0 1 N N N -2.700 -4.468 26.072 -2.736 3.291 -0.581 H13 IKS 32 IKS H14 H14 H 0 1 N N N -0.481 -4.877 25.166 -1.051 1.581 -0.100 H14 IKS 33 IKS OP3 OP3 O 0 1 N N N -0.398 -8.379 24.486 4.574 1.652 0.990 OP3 IKS 34 IKS H1 H1 H 0 1 N N N 0.039 -9.190 24.256 3.944 2.219 1.455 H1 IKS 35 # 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 IKS SE4 "C1'" SING N N 1 IKS SE4 "C4'" SING N N 2 IKS O2 C2 DOUB N N 3 IKS "C1'" N1 SING N N 4 IKS "C1'" "C2'" SING N N 5 IKS C2 N1 SING N N 6 IKS C2 N3 SING N N 7 IKS N1 C6 SING N N 8 IKS "O2'" "C2'" SING N N 9 IKS "C4'" "C5'" SING N N 10 IKS "C4'" "C3'" SING N N 11 IKS N3 C4 DOUB N N 12 IKS "C2'" "C3'" SING N N 13 IKS C6 C5 DOUB N N 14 IKS "C5'" "O5'" SING N N 15 IKS C4 C5 SING N N 16 IKS C4 N4 SING N N 17 IKS "O5'" P SING N N 18 IKS "C3'" "O3'" SING N N 19 IKS P OP1 DOUB N N 20 IKS P OP2 SING N N 21 IKS OP2 H2 SING N N 22 IKS "C5'" H3 SING N N 23 IKS "C5'" H4 SING N N 24 IKS "C4'" H5 SING N N 25 IKS "C3'" H6 SING N N 26 IKS "O3'" H7 SING N N 27 IKS "C2'" H8 SING N N 28 IKS "O2'" H9 SING N N 29 IKS "C1'" H10 SING N N 30 IKS N4 H11 SING N N 31 IKS N4 H12 SING N N 32 IKS C5 H13 SING N N 33 IKS C6 H14 SING N N 34 IKS P OP3 SING N N 35 IKS OP3 H1 SING N N 36 # 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 IKS InChI InChI 1.06 "InChI=1S/C9H14N3O7PSe/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(21-8)3-19-20(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1" IKS InChIKey InChI 1.06 PXFLZUCOUFTIFX-XVFCMESISA-N IKS SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@@H]2[Se][C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O" IKS SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2[Se][CH](CO[P](O)(O)=O)[CH](O)[CH]2O" IKS SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H]([Se]2)COP(=O)(O)O)O)O" IKS SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)C2C(C(C([Se]2)COP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id IKS _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-(4-azanyl-2-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 IKS "Create component" 2022-07-07 PDBJ IKS "Initial release" 2023-05-03 RCSB #