data_XUG # _chem_comp.id XUG _chem_comp.name "2'-SE-METHYL-2'-SELENOGUANOSINE 5'-(DIHYDROGEN PHOSPHATE)" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H16 N5 O7 P Se" _chem_comp.mon_nstd_parent_comp_id DG _chem_comp.pdbx_synonyms "(D)-2'-METHYLSELENYL-2'-DEOXYGUANOSINE-5'-PHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-05-18 _chem_comp.pdbx_modified_date 2021-03-01 _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 440.208 _chem_comp.one_letter_code G _chem_comp.three_letter_code XUG _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 2H1M _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 XUG O6 O6 O 0 1 N N N -18.257 31.299 -11.601 ? ? ? O6 XUG 1 XUG C6 C6 C 0 1 N N N -19.088 32.231 -11.552 ? ? ? C6 XUG 2 XUG C5 C5 C 0 1 Y N N -18.686 33.526 -11.233 ? ? ? C5 XUG 3 XUG N7 N7 N 0 1 Y N N -17.498 34.090 -10.936 ? ? ? N7 XUG 4 XUG C8 C8 C 0 1 Y N N -17.715 35.407 -10.713 ? ? ? C8 XUG 5 XUG N1 N1 N 0 1 N N N -20.394 31.984 -11.804 ? ? ? N1 XUG 6 XUG C2 C2 C 0 1 N N N -21.306 32.983 -11.751 ? ? ? C2 XUG 7 XUG N2 N2 N 0 1 N N N -22.610 32.736 -12.004 ? ? ? N2 XUG 8 XUG N3 N3 N 0 1 N N N -20.932 34.243 -11.447 ? ? ? N3 XUG 9 XUG C4 C4 C 0 1 Y N N -19.637 34.531 -11.187 ? ? ? C4 XUG 10 XUG N9 N9 N 0 1 Y N N -19.020 35.668 -10.869 ? ? ? N9 XUG 11 XUG "C1'" C1* C 0 1 N N R -19.687 36.984 -10.714 ? ? ? "C1'" XUG 12 XUG "O4'" O4* O 0 1 N N N -18.713 38.002 -10.463 ? ? ? "O4'" XUG 13 XUG "C2'" C2* C 0 1 N N R -20.595 36.927 -9.502 ? ? ? "C2'" XUG 14 XUG "SE2'" SE2* SE 0 0 N N N -22.176 38.045 -9.828 ? ? ? "SE2'" XUG 15 XUG "CA'" CA* C 0 1 N N N -23.247 36.750 -10.859 ? ? ? "CA'" XUG 16 XUG "C3'" C3* C 0 1 N N R -19.755 37.550 -8.418 ? ? ? "C3'" XUG 17 XUG "O3'" O3* O 0 1 N N N -20.493 38.205 -7.391 ? ? ? "O3'" XUG 18 XUG "C4'" C4* C 0 1 N N R -18.886 38.535 -9.150 ? ? ? "C4'" XUG 19 XUG "C5'" C5* C 0 1 N N N -17.574 38.633 -8.410 ? ? ? "C5'" XUG 20 XUG "O5'" O5* O 0 1 N N N -16.756 39.517 -9.143 ? ? ? "O5'" XUG 21 XUG P P P 0 1 N N N -15.215 39.144 -9.284 ? ? ? P XUG 22 XUG OP1 O1P O 0 1 N N N -14.481 39.930 -8.225 ? ? ? OP1 XUG 23 XUG OP2 O2P O 0 1 N N N -15.095 37.637 -9.334 ? ? ? OP2 XUG 24 XUG OP3 O3P O 0 1 N Y N -14.573 39.529 -10.491 ? ? ? OP3 XUG 25 XUG H8 H8 H 0 1 N N N -16.958 36.131 -10.451 ? ? ? H8 XUG 26 XUG HN1 HN1 H 0 1 N N N -20.688 31.056 -12.031 ? ? ? HN1 XUG 27 XUG HN21 1HN2 H 0 0 N N N -22.742 31.767 -12.215 ? ? ? HN21 XUG 28 XUG HN22 2HN2 H 0 0 N N N -23.337 33.422 -11.983 ? ? ? HN22 XUG 29 XUG "H1'" H1* H 0 1 N N N -20.248 37.209 -11.633 ? ? ? "H1'" XUG 30 XUG "H2'" H2* H 0 1 N N N -20.944 35.913 -9.257 ? ? ? "H2'" XUG 31 XUG "HA'1" 1HA* H 0 0 N N N -23.446 37.155 -11.862 ? ? ? "HA'1" XUG 32 XUG "HA'2" 2HA* H 0 0 N N N -22.692 35.805 -10.949 ? ? ? "HA'2" XUG 33 XUG "HA'3" 3HA* H 0 0 N N N -24.200 36.568 -10.341 ? ? ? "HA'3" XUG 34 XUG "H3'" H3* H 0 1 N N N -19.200 36.769 -7.877 ? ? ? "H3'" XUG 35 XUG "HO3'" H3T H 0 0 N Y N -19.930 38.351 -6.640 ? ? ? "HO3'" XUG 36 XUG "H4'" H4* H 0 1 N N N -19.318 39.545 -9.210 ? ? ? "H4'" XUG 37 XUG "H5'" 1H5* H 0 1 N N N -17.737 39.017 -7.392 ? ? ? "H5'" XUG 38 XUG "H5''" 2H5* H 0 0 N N N -17.100 37.645 -8.318 ? ? ? "H5''" XUG 39 XUG HOP2 2HOP H 0 0 N N N -14.175 37.414 -9.418 ? ? ? HOP2 XUG 40 XUG HOP3 3HOP H 0 0 N N N -15.220 39.615 -11.181 ? ? ? HOP3 XUG 41 # # 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 XUG O6 C6 DOUB N N 1 XUG C6 C5 SING N N 2 XUG C6 N1 SING N N 3 XUG C5 N7 SING Y N 4 XUG C5 C4 DOUB Y N 5 XUG N7 C8 DOUB Y N 6 XUG C8 N9 SING Y N 7 XUG C8 H8 SING N N 8 XUG N1 C2 SING N N 9 XUG N1 HN1 SING N N 10 XUG C2 N2 SING N N 11 XUG C2 N3 DOUB N N 12 XUG N2 HN21 SING N N 13 XUG N2 HN22 SING N N 14 XUG N3 C4 SING N N 15 XUG C4 N9 SING Y N 16 XUG N9 "C1'" SING N N 17 XUG "C1'" "O4'" SING N N 18 XUG "C1'" "C2'" SING N N 19 XUG "C1'" "H1'" SING N N 20 XUG "O4'" "C4'" SING N N 21 XUG "C2'" "SE2'" SING N N 22 XUG "C2'" "C3'" SING N N 23 XUG "C2'" "H2'" SING N N 24 XUG "SE2'" "CA'" SING N N 25 XUG "CA'" "HA'1" SING N N 26 XUG "CA'" "HA'2" SING N N 27 XUG "CA'" "HA'3" SING N N 28 XUG "C3'" "O3'" SING N N 29 XUG "C3'" "C4'" SING N N 30 XUG "C3'" "H3'" SING N N 31 XUG "O3'" "HO3'" SING N N 32 XUG "C4'" "C5'" SING N N 33 XUG "C4'" "H4'" SING N N 34 XUG "C5'" "O5'" SING N N 35 XUG "C5'" "H5'" SING N N 36 XUG "C5'" "H5''" SING N N 37 XUG "O5'" P SING N N 38 XUG P OP1 DOUB N N 39 XUG P OP2 SING N N 40 XUG P OP3 SING N N 41 XUG OP2 HOP2 SING N N 42 XUG OP3 HOP3 SING N N 43 # # 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 XUG SMILES ACDLabs 10.04 "O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3[Se]C)COP(=O)(O)O" XUG SMILES_CANONICAL CACTVS 3.341 "C[Se][C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1n2cnc3C(=O)NC(=Nc23)N" XUG SMILES CACTVS 3.341 "C[Se][CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1n2cnc3C(=O)NC(=Nc23)N" XUG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[Se][C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2N=C(NC3=O)N)COP(=O)(O)O)O" XUG SMILES "OpenEye OEToolkits" 1.5.0 "C[Se]C1C(C(OC1n2cnc3c2N=C(NC3=O)N)COP(=O)(O)O)O" XUG InChI InChI 1.03 "InChI=1S/C11H16N5O7PSe/c1-25-7-6(17)4(2-22-24(19,20)21)23-10(7)16-3-13-5-8(16)14-11(12)15-9(5)18/h3-4,6-7,10,17H,2H2,1H3,(H2,19,20,21)(H3,12,14,15,18)/t4-,6-,7-,10-/m1/s1" XUG InChIKey InChI 1.03 VGEIDTKNQDSGED-KQYNXXCUSA-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 XUG "SYSTEMATIC NAME" ACDLabs 10.04 "2'-Se-methyl-2'-selenoguanosine 5'-(dihydrogen phosphate)" XUG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-5-(2-amino-6-oxo-1H-purin-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 XUG "Create component" 2006-05-18 RCSB XUG "Modify descriptor" 2011-06-04 RCSB XUG "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id XUG _pdbx_chem_comp_synonyms.name "(D)-2'-METHYLSELENYL-2'-DEOXYGUANOSINE-5'-PHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##