data_8GA # _chem_comp.id 8GA _chem_comp.name 5-Se-methyl-5-seleno-alpha-D-ribofuranose _chem_comp.type "D-saccharide, alpha 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-alpha-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 8GA _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 8GA 5-Se-methyl-5-seleno-alpha-D-ribose PDB ? 2 8GA 5-Se-methyl-5-seleno-D-ribose PDB ? 3 8GA 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 8GA CS CS C 0 1 N N N 43.509 34.506 8.765 3.790 0.269 0.803 CS 8GA 1 8GA C5 "C5'" C 0 1 N N N 41.381 32.760 8.279 0.802 0.689 0.598 C5 8GA 2 8GA C4 "C4'" C 0 1 N N S 40.671 31.420 8.549 -0.511 0.426 -0.143 C4 8GA 3 8GA O4 "O4'" O 0 1 N N N 39.945 31.449 9.762 -0.853 -0.961 -0.048 O4 8GA 4 8GA C1 "C1'" C 0 1 N N S 38.953 30.387 9.664 -2.100 -1.113 0.649 C1 8GA 5 8GA O1 "O1'" O 0 1 N Y N 39.568 29.177 10.038 -2.859 -2.183 0.081 O1 8GA 6 8GA C2 "C2'" C 0 1 N N R 38.513 30.299 8.261 -2.839 0.234 0.452 C2 8GA 7 8GA O2 "O2'" O 0 1 N N N 38.452 28.930 7.790 -3.492 0.283 -0.818 O2 8GA 8 8GA C3 "C3'" C 0 1 N N S 39.586 31.143 7.432 -1.652 1.234 0.512 C3 8GA 9 8GA O3 "O3'" O 0 1 N N N 40.246 30.384 6.396 -1.941 2.412 -0.244 O3 8GA 10 8GA SE SE SE 0 1 N N N 42.649 33.123 9.641 2.268 -0.224 -0.329 SE 8GA 11 8GA H1A H1 H 0 1 N N N 44.322 34.892 9.397 3.895 1.354 0.820 H1A 8GA 12 8GA H2A H2 H 0 1 N N N 43.926 34.136 7.817 3.622 -0.095 1.817 H2A 8GA 13 8GA H3A H3 H 0 1 N N N 42.790 35.313 8.560 4.701 -0.177 0.403 H3A 8GA 14 8GA H51 H4 H 0 1 N N N 41.896 32.708 7.309 0.998 1.761 0.620 H51 8GA 15 8GA H52 H5 H 0 1 N N N 40.634 33.567 8.255 0.726 0.312 1.617 H52 8GA 16 8GA H4 H6 H 0 1 N N N 41.409 30.604 8.542 -0.408 0.711 -1.190 H4 8GA 17 8GA H1 H7 H 0 1 N N N 38.094 30.609 10.314 -1.921 -1.297 1.708 H1 8GA 18 8GA HO1 H8 H 0 1 N Y N 39.852 29.232 10.943 -2.424 -3.045 0.136 HO1 8GA 19 8GA H2 H9 H 0 1 N N N 37.532 30.783 8.147 -3.547 0.416 1.262 H2 8GA 20 8GA HO2 H10 H 0 1 N Y N 37.809 28.449 8.297 -4.169 -0.396 -0.939 HO2 8GA 21 8GA H3 H11 H 0 1 N N N 39.147 32.083 7.067 -1.407 1.484 1.544 H3 8GA 22 8GA HO3 H12 H 0 1 N Y N 40.868 30.941 5.943 -2.707 2.907 0.077 HO3 8GA 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 8GA O3 C3 SING N N 1 8GA C3 C2 SING N N 2 8GA C3 C4 SING N N 3 8GA O2 C2 SING N N 4 8GA C2 C1 SING N N 5 8GA C5 C4 SING N N 6 8GA C5 SE SING N N 7 8GA C4 O4 SING N N 8 8GA CS SE SING N N 9 8GA C1 O4 SING N N 10 8GA C1 O1 SING N N 11 8GA CS H1A SING N N 12 8GA CS H2A SING N N 13 8GA CS H3A SING N N 14 8GA C5 H51 SING N N 15 8GA C5 H52 SING N N 16 8GA C4 H4 SING N N 17 8GA C1 H1 SING N N 18 8GA O1 HO1 SING N N 19 8GA C2 H2 SING N N 20 8GA O2 HO2 SING N N 21 8GA C3 H3 SING N N 22 8GA O3 HO3 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 8GA SMILES ACDLabs 12.01 "C[Se]CC1OC(O)C(O)C1O" 8GA 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" 8GA InChIKey InChI 1.03 UFNQFLPLDXICBS-KAZBKCHUSA-N 8GA SMILES_CANONICAL CACTVS 3.385 "C[Se]C[C@H]1O[C@H](O)[C@H](O)[C@@H]1O" 8GA SMILES CACTVS 3.385 "C[Se]C[CH]1O[CH](O)[CH](O)[CH]1O" 8GA SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C[Se]C[C@@H]1[C@H]([C@H]([C@H](O1)O)O)O" 8GA 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 8GA "SYSTEMATIC NAME" ACDLabs 12.01 5-Se-methyl-5-seleno-alpha-D-ribofuranose 8GA "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{S},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 8GA "CARBOHYDRATE ISOMER" D PDB ? 8GA "CARBOHYDRATE RING" furanose PDB ? 8GA "CARBOHYDRATE ANOMER" alpha PDB ? 8GA "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 8GA "Create component" 2017-02-04 RCSB 8GA "Initial release" 2018-09-12 RCSB 8GA "Other modification" 2020-07-03 RCSB 8GA "Modify synonyms" 2020-07-17 RCSB 8GA "Modify linking type" 2020-07-17 RCSB 8GA "Modify atom id" 2020-07-17 RCSB 8GA "Modify component atom id" 2020-07-17 RCSB 8GA "Modify leaving atom flag" 2020-07-17 RCSB ##