data_2ST # _chem_comp.id 2ST _chem_comp.name "5-METHYL-2'-SE-METHYL-2'-SELENOURIDINE 5'-(DIHYDROGEN PHOSPHATE)" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H17 N2 O8 P Se" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-06-16 _chem_comp.pdbx_modified_date 2011-06-04 _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 415.195 _chem_comp.one_letter_code T _chem_comp.three_letter_code 2ST _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag Y _chem_comp.pdbx_model_coordinates_db_code 2HC7 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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 2ST OP3 O3P O 0 1 N Y N 13.078 17.334 8.037 ? ? ? OP3 2ST 1 2ST P P P 0 1 N N N 13.492 18.302 6.818 ? ? ? P 2ST 2 2ST OP1 O1P O 0 1 N N N 14.306 17.452 5.940 ? ? ? OP1 2ST 3 2ST OP2 O2P O 0 1 N N N 14.011 19.605 7.325 ? ? ? OP2 2ST 4 2ST "O5'" O5* O 0 1 N N N 12.128 18.602 6.054 ? ? ? "O5'" 2ST 5 2ST N1 N1 N 0 1 N N N 8.711 20.572 6.456 ? ? ? N1 2ST 6 2ST C6 C6 C 0 1 N N N 9.940 20.729 7.083 ? ? ? C6 2ST 7 2ST C2 C2 C 0 1 N N N 7.716 21.533 6.581 ? ? ? C2 2ST 8 2ST O2 O2 O 0 1 N N N 6.658 21.447 5.980 ? ? ? O2 2ST 9 2ST N3 N3 N 0 1 N N N 7.993 22.604 7.392 ? ? ? N3 2ST 10 2ST C4 C4 C 0 1 N N N 9.167 22.860 8.082 ? ? ? C4 2ST 11 2ST O4 O4 O 0 1 N N N 9.259 23.857 8.783 ? ? ? O4 2ST 12 2ST C5 C5 C 0 1 N N N 10.242 21.831 7.892 ? ? ? C5 2ST 13 2ST C5A C5A C 0 1 N N N 11.566 22.027 8.577 ? ? ? C5A 2ST 14 2ST "C2'" C2* C 0 1 N N R 8.678 19.771 4.177 ? ? ? "C2'" 2ST 15 2ST "C5'" C5* C 0 1 N N N 11.439 17.552 5.404 ? ? ? "C5'" 2ST 16 2ST "C4'" C4* C 0 1 N N R 10.121 18.045 4.868 ? ? ? "C4'" 2ST 17 2ST "O4'" O4* O 0 1 N N N 9.296 18.390 6.002 ? ? ? "O4'" 2ST 18 2ST "C1'" C1* C 0 1 N N R 8.347 19.399 5.594 ? ? ? "C1'" 2ST 19 2ST "C3'" C3* C 0 1 N N R 10.134 19.347 4.096 ? ? ? "C3'" 2ST 20 2ST SE SE SE 0 0 N N N 7.479 18.552 3.031 ? ? ? SE 2ST 21 2ST "CA'" CA* C 0 1 N N N 5.814 19.584 3.086 ? ? ? "CA'" 2ST 22 2ST "O3'" O3* O 0 1 N N N 10.480 19.203 2.780 ? ? ? "O3'" 2ST 23 2ST HOP3 3HOP H 0 0 N N N 12.551 17.884 8.605 ? ? ? HOP3 2ST 24 2ST HOP2 2HOP H 0 0 N N N 14.255 20.176 6.606 ? ? ? HOP2 2ST 25 2ST H6 H6 H 0 1 N N N 10.694 19.969 6.941 ? ? ? H6 2ST 26 2ST HN3 HN3 H 0 1 N N N 7.262 23.279 7.498 ? ? ? HN3 2ST 27 2ST H5A1 1H5A H 0 0 N N N 12.366 22.075 7.823 ? ? ? H5A1 2ST 28 2ST H5A2 2H5A H 0 0 N N N 11.546 22.965 9.151 ? ? ? H5A2 2ST 29 2ST H5A3 3H5A H 0 0 N N N 11.754 21.184 9.258 ? ? ? H5A3 2ST 30 2ST "H2'" H2* H 0 1 N N N 8.532 20.816 3.866 ? ? ? "H2'" 2ST 31 2ST "H5'" 1H5* H 0 1 N N N 11.256 16.740 6.123 ? ? ? "H5'" 2ST 32 2ST "H5''" 2H5* H 0 0 N N N 12.052 17.186 4.567 ? ? ? "H5''" 2ST 33 2ST "H4'" H4* H 0 1 N N N 9.792 17.233 4.203 ? ? ? "H4'" 2ST 34 2ST "H1'" H1* H 0 1 N N N 7.295 19.088 5.675 ? ? ? "H1'" 2ST 35 2ST "H3'" H3* H 0 1 N N N 10.870 20.054 4.506 ? ? ? "H3'" 2ST 36 2ST "HA'1" 1HA* H 0 0 N N N 5.536 19.777 4.133 ? ? ? "HA'1" 2ST 37 2ST "HA'2" 2HA* H 0 0 N N N 5.958 20.541 2.562 ? ? ? "HA'2" 2ST 38 2ST "HA'3" 3HA* H 0 0 N N N 5.013 19.013 2.594 ? ? ? "HA'3" 2ST 39 2ST "HO3'" H3T H 0 0 N Y N 9.694 19.170 2.247 ? ? ? "HO3'" 2ST 40 # # 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 2ST OP3 P SING N N 1 2ST OP3 HOP3 SING N N 2 2ST P OP1 DOUB N N 3 2ST P OP2 SING N N 4 2ST P "O5'" SING N N 5 2ST OP2 HOP2 SING N N 6 2ST "O5'" "C5'" SING N N 7 2ST N1 C6 SING N N 8 2ST N1 C2 SING N N 9 2ST N1 "C1'" SING N N 10 2ST C6 C5 DOUB N N 11 2ST C6 H6 SING N N 12 2ST C2 O2 DOUB N N 13 2ST C2 N3 SING N N 14 2ST N3 C4 SING N N 15 2ST N3 HN3 SING N N 16 2ST C4 O4 DOUB N N 17 2ST C4 C5 SING N N 18 2ST C5 C5A SING N N 19 2ST C5A H5A1 SING N N 20 2ST C5A H5A2 SING N N 21 2ST C5A H5A3 SING N N 22 2ST "C2'" "C1'" SING N N 23 2ST "C2'" "C3'" SING N N 24 2ST "C2'" SE SING N N 25 2ST "C2'" "H2'" SING N N 26 2ST "C5'" "C4'" SING N N 27 2ST "C5'" "H5'" SING N N 28 2ST "C5'" "H5''" SING N N 29 2ST "C4'" "O4'" SING N N 30 2ST "C4'" "C3'" SING N N 31 2ST "C4'" "H4'" SING N N 32 2ST "O4'" "C1'" SING N N 33 2ST "C1'" "H1'" SING N N 34 2ST "C3'" "O3'" SING N N 35 2ST "C3'" "H3'" SING N N 36 2ST SE "CA'" SING N N 37 2ST "CA'" "HA'1" SING N N 38 2ST "CA'" "HA'2" SING N N 39 2ST "CA'" "HA'3" SING N N 40 2ST "O3'" "HO3'" SING N N 41 # # 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 2ST SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2[Se]C)COP(=O)(O)O" 2ST SMILES_CANONICAL CACTVS 3.341 "C[Se][C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O" 2ST SMILES CACTVS 3.341 "C[Se][CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O" 2ST SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)[Se]C" 2ST SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)[Se]C" 2ST InChI InChI 1.03 "InChI=1S/C11H17N2O8PSe/c1-5-3-13(11(16)12-9(5)15)10-8(23-2)7(14)6(21-10)4-20-22(17,18)19/h3,6-8,10,14H,4H2,1-2H3,(H,12,15,16)(H2,17,18,19)/t6-,7-,8-,10-/m1/s1" 2ST InChIKey InChI 1.03 KLYIIOBIPBBIGV-FDDDBJFASA-N # # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier 2ST "SYSTEMATIC NAME" ACDLabs 10.04 "5-methyl-2'-Se-methyl-2'-selenouridine 5'-(dihydrogen phosphate)" 2ST "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-4-methylselanyl-oxolan-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 2ST "Create component" 2006-06-16 RCSB 2ST "Modify descriptor" 2011-06-04 RCSB ##