data_8GG # _chem_comp.id 8GG _chem_comp.name 5-Se-methyl-5-seleno-beta-D-ribofuranose _chem_comp.type "D-saccharide, beta linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C6 H12 O4 Se" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "5-Se-methyl-5-seleno-beta-D-ribose; 5-Se-methyl-5-seleno-D-ribose; 5-Se-methyl-5-seleno-ribose" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-02-04 _chem_comp.pdbx_modified_date 2020-07-17 _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 227.117 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 8GG _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 5ULB _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 8GG 5-Se-methyl-5-seleno-beta-D-ribose PDB ? 2 8GG 5-Se-methyl-5-seleno-D-ribose PDB ? 3 8GG 5-Se-methyl-5-seleno-ribose PDB ? # # 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 8GG O4 "O4'" O 0 1 N N N 40.007 31.416 9.730 0.790 1.027 0.032 O4 8GG 1 8GG C5 "C5'" C 0 1 N N N 41.379 32.818 8.285 -0.830 -0.723 0.562 C5 8GG 2 8GG C4 "C4'" C 0 1 N N S 40.699 31.464 8.525 0.473 -0.370 -0.157 C4 8GG 3 8GG C3 "C3'" C 0 1 N N S 39.625 31.121 7.421 1.660 -1.132 0.474 C3 8GG 4 8GG O3 "O3'" O 0 1 N N N 40.219 30.376 6.390 1.974 -2.294 -0.296 O3 8GG 5 8GG C2 "C2'" C 0 1 N N R 38.626 30.270 8.308 2.826 -0.119 0.425 C2 8GG 6 8GG O2 "O2'" O 0 1 N N N 38.423 28.935 7.815 3.895 -0.625 -0.377 O2 8GG 7 8GG C1 "C1'" C 0 1 N N R 39.312 30.190 9.570 2.206 1.135 -0.230 C1 8GG 8 8GG O1 "O1'" O 0 1 N Y N 38.369 30.193 10.610 2.733 2.321 0.369 O1 8GG 9 8GG SE SE SE 0 1 N N N 42.651 33.120 9.640 -2.324 0.212 -0.295 SE 8GG 10 8GG CS CS C 0 1 N N N 43.542 34.499 8.772 -3.829 -0.405 0.799 CS 8GG 11 8GG H51 H1 H 0 1 N N N 41.880 32.810 7.306 -0.995 -1.799 0.507 H51 8GG 12 8GG H52 H2 H 0 1 N N N 40.624 33.618 8.304 -0.762 -0.419 1.607 H52 8GG 13 8GG H4 H3 H 0 1 N N N 41.471 30.681 8.497 0.394 -0.600 -1.220 H4 8GG 14 8GG H3 H4 H 0 1 N N N 39.134 32.038 7.064 1.434 -1.405 1.504 H3 8GG 15 8GG HO3 H5 H 0 1 N Y N 40.805 30.934 5.893 2.749 -2.778 0.021 HO3 8GG 16 8GG H2 H6 H 0 1 N N N 37.673 30.811 8.404 3.176 0.109 1.431 H2 8GG 17 8GG HO2 H7 H 0 1 N Y N 37.818 28.475 8.385 4.654 -0.029 -0.442 HO2 8GG 18 8GG H1 H8 H 0 1 N N N 39.985 29.321 9.616 2.394 1.135 -1.303 H1 8GG 19 8GG HO1 H9 H 0 1 N Y N 38.818 30.140 11.445 2.379 3.140 -0.003 HO1 8GG 20 8GG H10 H10 H 0 1 N N N 44.369 34.856 9.403 -3.902 -1.491 0.736 H10 8GG 21 8GG H11 H11 H 0 1 N N N 43.943 34.132 7.816 -3.669 -0.111 1.836 H11 8GG 22 8GG H12 H12 H 0 1 N N N 42.842 35.326 8.583 -4.752 0.043 0.432 H12 8GG 23 # # 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 8GG O3 C3 SING N N 1 8GG C3 C2 SING N N 2 8GG C3 C4 SING N N 3 8GG O2 C2 SING N N 4 8GG C5 C4 SING N N 5 8GG C5 SE SING N N 6 8GG C2 C1 SING N N 7 8GG C4 O4 SING N N 8 8GG CS SE SING N N 9 8GG C1 O4 SING N N 10 8GG C1 O1 SING N N 11 8GG C5 H51 SING N N 12 8GG C5 H52 SING N N 13 8GG C4 H4 SING N N 14 8GG C3 H3 SING N N 15 8GG O3 HO3 SING N N 16 8GG C2 H2 SING N N 17 8GG O2 HO2 SING N N 18 8GG C1 H1 SING N N 19 8GG O1 HO1 SING N N 20 8GG CS H10 SING N N 21 8GG CS H11 SING N N 22 8GG CS H12 SING N N 23 # # 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 8GG SMILES ACDLabs 12.01 "O1C(C[Se]C)C(C(C1O)O)O" 8GG InChI InChI 1.03 "InChI=1S/C6H12O4Se/c1-11-2-3-4(7)5(8)6(9)10-3/h3-9H,2H2,1H3/t3-,4-,5-,6-/m1/s1" 8GG InChIKey InChI 1.03 UFNQFLPLDXICBS-KVTDHHQDSA-N 8GG SMILES_CANONICAL CACTVS 3.385 "C[Se]C[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O" 8GG SMILES CACTVS 3.385 "C[Se]C[CH]1O[CH](O)[CH](O)[CH]1O" 8GG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C[Se]C[C@@H]1[C@H]([C@H]([C@@H](O1)O)O)O" 8GG SMILES "OpenEye OEToolkits" 2.0.6 "C[Se]CC1C(C(C(O1)O)O)O" # # 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 8GG "SYSTEMATIC NAME" ACDLabs 12.01 5-Se-methyl-5-seleno-beta-D-ribofuranose 8GG "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{R},3~{R},4~{S},5~{S})-5-(methylselanylmethyl)oxolane-2,3,4-triol" # # loop_ _pdbx_chem_comp_feature.comp_id _pdbx_chem_comp_feature.type _pdbx_chem_comp_feature.value _pdbx_chem_comp_feature.source _pdbx_chem_comp_feature.support 8GG "CARBOHYDRATE ISOMER" D PDB ? 8GG "CARBOHYDRATE RING" furanose PDB ? 8GG "CARBOHYDRATE ANOMER" beta PDB ? 8GG "CARBOHYDRATE PRIMARY CARBONYL GROUP" aldose PDB ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 8GG "Create component" 2017-02-04 RCSB 8GG "Initial release" 2018-09-12 RCSB 8GG "Other modification" 2020-07-03 RCSB 8GG "Modify synonyms" 2020-07-17 RCSB 8GG "Modify linking type" 2020-07-17 RCSB 8GG "Modify atom id" 2020-07-17 RCSB 8GG "Modify component atom id" 2020-07-17 RCSB 8GG "Modify leaving atom flag" 2020-07-17 RCSB ##