data_Z9D # _chem_comp.id Z9D _chem_comp.name 4-deoxy-beta-D-xylo-hexopyranose _chem_comp.type "D-saccharide, beta linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C6 H12 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-12-17 _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 164.156 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Z9D _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 1GA8 _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 Z9D C1 C1 C 0 1 N N R 22.025 53.821 65.773 0.454 1.236 -0.244 C1 Z9D 1 Z9D C2 C2 C 0 1 N N R 22.285 52.460 65.211 1.490 0.209 0.220 C2 Z9D 2 Z9D C3 C3 C 0 1 N N S 22.302 51.487 66.383 1.096 -1.176 -0.302 C3 Z9D 3 Z9D C4 C4 C 0 1 N N N 23.469 51.896 67.335 -0.316 -1.511 0.189 C4 Z9D 4 Z9D C5 C5 C 0 1 N N S 23.349 53.194 67.910 -1.282 -0.419 -0.274 C5 Z9D 5 Z9D C6 C6 C 0 1 N N N 24.315 53.629 68.705 -2.684 -0.715 0.264 C6 Z9D 6 Z9D O1 O1 O 0 1 N Y N 21.781 55.096 65.145 0.785 2.521 0.286 O1 Z9D 7 Z9D O2 O2 O 0 1 N N N 21.240 52.137 64.311 2.777 0.564 -0.292 O2 Z9D 8 Z9D O3 O3 O 0 1 N N N 22.547 50.210 65.851 2.017 -2.152 0.188 O3 Z9D 9 Z9D O5 O5 O 0 1 N N N 23.097 54.158 66.749 -0.840 0.847 0.220 O5 Z9D 10 Z9D O6 O6 O 0 1 N N N 24.696 52.835 69.870 -3.608 0.239 -0.264 O6 Z9D 11 Z9D HO1 HO1 H 0 1 N Y N 21.654 55.759 65.813 0.169 3.222 0.032 HO1 Z9D 12 Z9D H1 H1 H 0 1 N N N 21.141 53.668 66.409 0.451 1.282 -1.333 H1 Z9D 13 Z9D H2 H2 H 0 1 N N N 23.262 52.444 64.705 1.523 0.192 1.309 H2 Z9D 14 Z9D H3 H3 H 0 1 N N N 21.347 51.531 66.927 1.111 -1.172 -1.392 H3 Z9D 15 Z9D H41 H41 H 0 1 N N N 23.515 51.163 68.154 -0.626 -2.471 -0.223 H41 Z9D 16 Z9D H42 H42 H 0 1 N N N 24.406 51.863 66.760 -0.319 -1.564 1.278 H42 Z9D 17 Z9D H5 H5 H 0 1 N N N 22.415 53.191 68.491 -1.309 -0.394 -1.364 H5 Z9D 18 Z9D H61 H61 H 0 1 N N N 25.216 53.739 68.084 -2.984 -1.718 -0.040 H61 Z9D 19 Z9D H62 H62 H 0 1 N N N 24.003 54.616 69.078 -2.676 -0.651 1.352 H62 Z9D 20 Z9D HO2 HO2 H 0 1 N N N 21.392 51.273 63.945 3.088 1.433 -0.005 HO2 Z9D 21 Z9D HO3 HO3 H 0 1 N N N 22.565 49.572 66.554 2.934 -1.997 -0.080 HO3 Z9D 22 Z9D HO6 HO6 H 0 1 N N N 25.397 53.274 70.338 -4.518 0.111 0.036 HO6 Z9D 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 Z9D C1 C2 SING N N 1 Z9D C1 O1 SING N N 2 Z9D C1 O5 SING N N 3 Z9D C1 H1 SING N N 4 Z9D C2 C3 SING N N 5 Z9D C2 O2 SING N N 6 Z9D C2 H2 SING N N 7 Z9D C3 C4 SING N N 8 Z9D C3 O3 SING N N 9 Z9D C3 H3 SING N N 10 Z9D C4 C5 SING N N 11 Z9D C4 H41 SING N N 12 Z9D C4 H42 SING N N 13 Z9D C5 C6 SING N N 14 Z9D C5 O5 SING N N 15 Z9D C5 H5 SING N N 16 Z9D C6 O6 SING N N 17 Z9D C6 H61 SING N N 18 Z9D C6 H62 SING N N 19 Z9D O2 HO2 SING N N 20 Z9D O3 HO3 SING N N 21 Z9D O6 HO6 SING N N 22 Z9D HO1 O1 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 Z9D SMILES ACDLabs 12.01 "OC1CC(OC(O)C1O)CO" Z9D InChI InChI 1.03 "InChI=1S/C6H12O5/c7-2-3-1-4(8)5(9)6(10)11-3/h3-10H,1-2H2/t3-,4-,5+,6+/m0/s1" Z9D InChIKey InChI 1.03 HDEMQQHXNOJATE-UNTFVMJOSA-N Z9D SMILES_CANONICAL CACTVS 3.370 "OC[C@@H]1C[C@H](O)[C@@H](O)[C@H](O)O1" Z9D SMILES CACTVS 3.370 "OC[CH]1C[CH](O)[CH](O)[CH](O)O1" Z9D SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1[C@H](O[C@H]([C@@H]([C@H]1O)O)O)CO" Z9D SMILES "OpenEye OEToolkits" 1.7.6 "C1C(OC(C(C1O)O)O)CO" # # 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 Z9D "SYSTEMATIC NAME" ACDLabs 12.01 4-deoxy-beta-D-xylo-hexopyranose Z9D "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2R,3R,4S,6S)-6-(hydroxymethyl)oxane-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 Z9D "CARBOHYDRATE ISOMER" D PDB ? Z9D "CARBOHYDRATE RING" pyranose PDB ? Z9D "CARBOHYDRATE ANOMER" beta PDB ? Z9D "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 Z9D "Create component" 2012-12-17 RCSB Z9D "Modify atom id" 2020-05-09 RCSB Z9D "Modify component atom id" 2020-07-17 RCSB Z9D "Initial release" 2020-07-29 RCSB ##