data_XYZ # _chem_comp.id XYZ _chem_comp.name beta-D-xylofuranose _chem_comp.type "D-saccharide, beta linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C5 H10 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "beta-D-xylose; D-xylose; xylose" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-06-10 _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 150.130 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XYZ _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 N _chem_comp.pdbx_model_coordinates_db_code 1W0Q _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 XYZ beta-D-xylose PDB ? 2 XYZ D-xylose PDB ? 3 XYZ xylose 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 XYZ C4 C4 C 0 1 N N R 11.700 -18.178 4.800 0.854 -0.125 0.500 C4 XYZ 1 XYZ O4 O O 0 1 N N N 12.486 -18.199 3.597 0.278 1.114 0.034 O4 XYZ 2 XYZ C1 C1 C 0 1 N N R 12.751 -19.561 3.214 -1.148 0.991 0.169 C1 XYZ 3 XYZ C2 C2 C 0 1 N N R 12.128 -20.456 4.317 -1.488 -0.510 0.085 C2 XYZ 4 XYZ O2 O2 O 0 1 N N N 10.826 -20.912 3.933 -2.148 -0.941 1.277 O2 XYZ 5 XYZ C3 C3 C 0 1 N N R 12.009 -19.510 5.505 -0.110 -1.206 -0.052 C3 XYZ 6 XYZ O3 O3 O 0 1 N N N 13.271 -19.465 6.169 0.182 -1.495 -1.421 O3 XYZ 7 XYZ C5 C5 C 0 1 N N N 12.007 -16.896 5.589 2.260 -0.314 -0.073 C5 XYZ 8 XYZ O5 O5 O 0 1 N N N 11.223 -16.840 6.781 3.142 0.653 0.501 O5 XYZ 9 XYZ O1 O1 O 0 1 N Y N 13.845 -19.749 3.106 -1.799 1.699 -0.888 O1 XYZ 10 XYZ H4 H4 H 0 1 N N N 10.612 -18.125 4.645 0.878 -0.152 1.589 H4 XYZ 11 XYZ H1 H1 H 0 1 N N N 12.310 -19.785 2.231 -1.465 1.389 1.133 H1 XYZ 12 XYZ H2 H2 H 0 1 N N N 12.727 -21.356 4.521 -2.108 -0.713 -0.788 H2 XYZ 13 XYZ HO2 HO2 H 0 1 N Y N 10.284 -21.013 4.707 -2.969 -0.434 1.340 HO2 XYZ 14 XYZ H3 H3 H 0 1 N N N 11.261 -19.781 6.264 -0.070 -2.113 0.551 H3 XYZ 15 XYZ HO3 HO3 H 0 1 N Y N 13.968 -19.455 5.524 -0.506 -2.098 -1.732 HO3 XYZ 16 XYZ H51 H51 H 0 1 N N N 11.763 -16.026 4.962 2.233 -0.183 -1.155 H51 XYZ 17 XYZ H52 H52 H 0 1 N N N 13.073 -16.886 5.859 2.617 -1.316 0.163 H52 XYZ 18 XYZ HO5 H5 H 0 1 N Y N 11.797 -16.828 7.538 4.015 0.500 0.114 HO5 XYZ 19 XYZ HO1 HO1 H 0 1 N Y N 14.068 -19.802 2.184 -1.548 2.628 -0.798 HO1 XYZ 20 # # 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 XYZ C4 O4 SING N N 1 XYZ C4 C3 SING N N 2 XYZ C4 C5 SING N N 3 XYZ C4 H4 SING N N 4 XYZ O4 C1 SING N N 5 XYZ C1 C2 SING N N 6 XYZ C1 O1 SING N N 7 XYZ C1 H1 SING N N 8 XYZ C2 O2 SING N N 9 XYZ C2 C3 SING N N 10 XYZ C2 H2 SING N N 11 XYZ O2 HO2 SING N N 12 XYZ C3 O3 SING N N 13 XYZ C3 H3 SING N N 14 XYZ O3 HO3 SING N N 15 XYZ C5 O5 SING N N 16 XYZ C5 H51 SING N N 17 XYZ C5 H52 SING N N 18 XYZ O5 HO5 SING N N 19 XYZ O1 HO1 SING N N 20 # # 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 XYZ SMILES ACDLabs 10.04 "OC1C(OC(O)C1O)CO" XYZ SMILES_CANONICAL CACTVS 3.341 "OC[C@H]1O[C@@H](O)[C@H](O)[C@H]1O" XYZ SMILES CACTVS 3.341 "OC[CH]1O[CH](O)[CH](O)[CH]1O" XYZ SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C([C@@H]1[C@@H]([C@H]([C@@H](O1)O)O)O)O" XYZ SMILES "OpenEye OEToolkits" 1.5.0 "C(C1C(C(C(O1)O)O)O)O" XYZ InChI InChI 1.03 "InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3+,4-,5-/m1/s1" XYZ InChIKey InChI 1.03 HMFHBZSHGGEWLO-KKQCNMDGSA-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 XYZ "SYSTEMATIC NAME" ACDLabs 10.04 beta-D-xylofuranose XYZ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,3R,4R,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol" XYZ "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DXylfb XYZ "COMMON NAME" GMML 1.0 b-D-xylofuranose XYZ "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 b-D-Xylf XYZ "SNFG CARBOHYDRATE SYMBOL" GMML 1.0 Xyl # # 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 XYZ "CARBOHYDRATE ISOMER" D PDB ? XYZ "CARBOHYDRATE RING" furanose PDB ? XYZ "CARBOHYDRATE ANOMER" beta PDB ? XYZ "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 XYZ "Create component" 2004-06-10 RCSB XYZ "Modify descriptor" 2011-06-04 RCSB XYZ "Other modification" 2019-08-12 RCSB XYZ "Other modification" 2019-12-19 RCSB XYZ "Other modification" 2020-07-03 RCSB XYZ "Modify name" 2020-07-17 RCSB XYZ "Modify synonyms" 2020-07-17 RCSB XYZ "Modify atom id" 2020-07-17 RCSB XYZ "Modify component atom id" 2020-07-17 RCSB ##