data_XUA # _chem_comp.id XUA _chem_comp.name ;2'-Se-methyl-2'-selenoadenosine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H16 N5 O6 P Se" _chem_comp.mon_nstd_parent_comp_id DA _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-07-27 _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 424.208 _chem_comp.one_letter_code A _chem_comp.three_letter_code XUA _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 3IFF _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 XUA P P P 0 1 N N N 50.935 20.715 -19.186 -5.123 -1.321 0.219 P XUA 1 XUA N1 N1 N 0 1 Y N N 43.970 23.610 -14.960 5.530 -1.612 0.564 N1 XUA 2 XUA C2 C2 C 0 1 Y N N 43.327 22.839 -15.857 4.992 -0.550 1.137 C2 XUA 3 XUA N3 N3 N 0 1 Y N N 43.883 22.090 -16.805 3.715 -0.254 1.018 N3 XUA 4 XUA C4 C4 C 0 1 Y N N 45.236 22.164 -16.797 2.904 -1.026 0.304 C4 XUA 5 XUA C5 C5 C 0 1 Y N N 46.026 22.913 -15.953 3.428 -2.168 -0.326 C5 XUA 6 XUA C6 C6 C 0 1 Y N N 45.327 23.674 -14.979 4.797 -2.443 -0.170 C6 XUA 7 XUA N6 N6 N 0 1 N N N 45.926 24.462 -14.076 5.369 -3.552 -0.767 N6 XUA 8 XUA N7 N7 N 0 1 Y N N 47.371 22.768 -16.271 2.403 -2.769 -0.978 N7 XUA 9 XUA C8 C8 C 0 1 Y N N 47.360 21.930 -17.271 1.311 -2.086 -0.793 C8 XUA 10 XUA N9 N9 N 0 1 Y N N 46.109 21.541 -17.647 1.568 -1.001 -0.009 N9 XUA 11 XUA "C1'" "C1'" C 0 1 N N R 45.739 20.585 -18.700 0.596 0.007 0.422 "C1'" XUA 12 XUA OP1 OP1 O 0 1 N N N 51.638 20.383 -20.424 -4.996 -2.353 -0.834 OP1 XUA 13 XUA "C2'" "C2'" C 0 1 N N R 45.454 21.185 -20.055 0.624 1.208 -0.542 "C2'" XUA 14 XUA "SE2'" "SE2'" SE 0 0 N N N 44.082 20.193 -21.070 1.107 2.847 0.417 "SE2'" XUA 15 XUA OP2 OP2 O 0 1 N N N 51.124 22.016 -18.498 -6.182 -0.203 -0.252 OP2 XUA 16 XUA "C3'" "C3'" C 0 1 N N R 46.829 21.048 -20.711 -0.825 1.298 -1.079 "C3'" XUA 17 XUA "O3'" "O3'" O 0 1 N N N 46.753 21.174 -22.127 -1.256 2.658 -1.160 "O3'" XUA 18 XUA OP3 OP3 O 0 1 N Y N 51.385 19.576 -18.185 -5.636 -2.005 1.583 OP3 XUA 19 XUA "C4'" "C4'" C 0 1 N N R 47.290 19.690 -20.207 -1.621 0.529 0.006 "C4'" XUA 20 XUA "O4'" "O4'" O 0 1 N N N 46.807 19.651 -18.851 -0.730 -0.546 0.383 "O4'" XUA 21 XUA "C5'" "C5'" C 0 1 N N N 48.787 19.467 -20.157 -2.923 -0.029 -0.574 "C5'" XUA 22 XUA "O5'" "O5'" O 0 1 N N N 49.359 20.520 -19.406 -3.691 -0.631 0.470 "O5'" XUA 23 XUA "CA'" "CA'" C 0 1 N N N 42.609 20.201 -19.788 1.059 4.160 -1.037 "CA'" XUA 24 XUA H2 H2 H 0 1 N N N 42.249 22.828 -15.801 5.624 0.099 1.725 H2 XUA 25 XUA HN6 HN6 H 0 1 N N N 45.233 24.899 -13.503 4.823 -4.151 -1.301 HN6 XUA 26 XUA HN6A HN6A H 0 0 N N N 46.533 23.911 -13.503 6.315 -3.731 -0.652 HN6A XUA 27 XUA H8 H8 H 0 1 N N N 48.258 21.577 -17.756 0.345 -2.341 -1.201 H8 XUA 28 XUA "H1'" "H1'" H 0 1 N N N 44.796 20.128 -18.366 0.830 0.338 1.434 "H1'" XUA 29 XUA "H2'" "H2'" H 0 1 N N N 45.049 22.207 -20.008 1.323 1.025 -1.359 "H2'" XUA 30 XUA HOP2 HOP2 H 0 0 N N N 51.744 22.546 -18.986 -6.316 0.507 0.391 HOP2 XUA 31 XUA "H3'" "H3'" H 0 1 N N N 47.547 21.840 -20.452 -0.912 0.805 -2.048 "H3'" XUA 32 XUA "HO3'" "HO3'" H 0 0 N Y N 47.622 21.084 -22.500 -2.158 2.766 -1.491 "HO3'" XUA 33 XUA HOP3 HOP3 H 0 0 N N N 51.980 18.982 -18.627 -6.496 -2.441 1.505 HOP3 XUA 34 XUA "H4'" "H4'" H 0 1 N N N 46.915 18.919 -20.896 -1.828 1.174 0.860 "H4'" XUA 35 XUA "H5'" "H5'" H 0 1 N N N 49.008 18.501 -19.679 -3.496 0.781 -1.026 "H5'" XUA 36 XUA "H5''" "H5'A" H 0 0 N N N 49.201 19.464 -21.176 -2.691 -0.777 -1.333 "H5''" XUA 37 XUA HA1 "HA'" H 0 1 N N N 41.746 19.672 -20.217 0.059 4.187 -1.470 HA1 XUA 38 XUA HA2 "HA'A" H 0 1 N N N 42.925 19.697 -18.863 1.313 5.145 -0.646 HA2 XUA 39 XUA HA3 "HA'B" H 0 1 N N N 42.326 21.240 -19.561 1.779 3.877 -1.805 HA3 XUA 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 XUA OP1 P DOUB N N 1 XUA "O5'" P SING N N 2 XUA P OP2 SING N N 3 XUA P OP3 SING N N 4 XUA C2 N1 DOUB Y N 5 XUA C6 N1 SING Y N 6 XUA N3 C2 SING Y N 7 XUA C2 H2 SING N N 8 XUA N3 C4 DOUB Y N 9 XUA N9 C4 SING Y N 10 XUA C4 C5 SING Y N 11 XUA N7 C5 SING Y N 12 XUA C5 C6 DOUB Y N 13 XUA C6 N6 SING N N 14 XUA N6 HN6 SING N N 15 XUA N6 HN6A SING N N 16 XUA C8 N7 DOUB Y N 17 XUA N9 C8 SING Y N 18 XUA C8 H8 SING N N 19 XUA "C1'" N9 SING N N 20 XUA "C2'" "C1'" SING N N 21 XUA "O4'" "C1'" SING N N 22 XUA "C1'" "H1'" SING N N 23 XUA "SE2'" "C2'" SING N N 24 XUA "C3'" "C2'" SING N N 25 XUA "C2'" "H2'" SING N N 26 XUA "SE2'" "CA'" SING N N 27 XUA OP2 HOP2 SING N N 28 XUA "O3'" "C3'" SING N N 29 XUA "C3'" "C4'" SING N N 30 XUA "C3'" "H3'" SING N N 31 XUA "O3'" "HO3'" SING N N 32 XUA OP3 HOP3 SING N N 33 XUA "C4'" "C5'" SING N N 34 XUA "C4'" "O4'" SING N N 35 XUA "C4'" "H4'" SING N N 36 XUA "C5'" "O5'" SING N N 37 XUA "C5'" "H5'" SING N N 38 XUA "C5'" "H5''" SING N N 39 XUA "CA'" HA1 SING N N 40 XUA "CA'" HA2 SING N N 41 XUA "CA'" HA3 SING N N 42 # 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 XUA SMILES ACDLabs 11.02 "O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C([Se]C)C3O" XUA SMILES_CANONICAL CACTVS 3.352 "C[Se][C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1n2cnc3c(N)ncnc23" XUA SMILES CACTVS 3.352 "C[Se][CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1n2cnc3c(N)ncnc23" XUA SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C[Se][C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2ncnc3N)COP(=O)(O)O)O" XUA SMILES "OpenEye OEToolkits" 1.7.0 "C[Se]C1C(C(OC1n2cnc3c2ncnc3N)COP(=O)(O)O)O" XUA InChI InChI 1.03 "InChI=1S/C11H16N5O6PSe/c1-24-8-7(17)5(2-21-23(18,19)20)22-11(8)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17H,2H2,1H3,(H2,12,13,14)(H2,18,19,20)/t5-,7-,8-,11-/m1/s1" XUA InChIKey InChI 1.03 BDEZXTBJEQTGCH-IOSLPCCCSA-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 XUA "SYSTEMATIC NAME" ACDLabs 11.02 ;2'-Se-methyl-2'-selenoadenosine 5'-(dihydrogen phosphate) ; XUA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-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 XUA "Create component" 2009-07-27 RCSB XUA "Modify aromatic_flag" 2011-06-04 RCSB XUA "Modify descriptor" 2011-06-04 RCSB #