data_XY9 # _chem_comp.id XY9 _chem_comp.name 2,3,4-tri-O-sulfo-beta-D-xylopyranose _chem_comp.type "D-saccharide, beta linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C5 H10 O14 S3" _chem_comp.mon_nstd_parent_comp_id XYP _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-08-09 _chem_comp.pdbx_modified_date 2023-11-06 _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 390.320 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XY9 _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 8E07 _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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 XY9 C2 C1 C 0 1 N N R N N N 21.031 4.958 -15.643 -1.365 -0.669 -0.122 C2 XY9 1 XY9 C5 C2 C 0 1 N N N N N N 23.072 6.603 -14.424 0.941 -2.221 -0.898 C5 XY9 2 XY9 C1 C3 C 0 1 N N R N N N 21.355 6.445 -16.001 -1.444 -1.971 -0.924 C1 XY9 3 XY9 C3 C4 C 0 1 N N S N N N 22.162 4.267 -14.839 -0.034 0.027 -0.423 C3 XY9 4 XY9 C4 C5 C 0 1 N N R N N N 22.943 5.184 -13.847 1.116 -0.930 -0.094 C4 XY9 5 XY9 O5 O1 O 0 1 N N N N N N 21.881 7.121 -14.905 -0.329 -2.801 -0.594 O5 XY9 6 XY9 O2 O2 O 0 1 N N N N N N 19.890 4.964 -14.858 -2.447 0.187 -0.493 O2 XY9 7 XY9 O34 O3 O 0 1 N N N N N N 18.112 5.176 -16.412 -4.694 0.835 -0.200 O34 XY9 8 XY9 O35 O4 O 0 1 N N N N N N 18.502 3.074 -15.460 -3.792 -1.290 0.757 O35 XY9 9 XY9 O36 O5 O 0 1 N N N N N N 17.553 4.780 -14.138 -3.315 0.812 1.712 O36 XY9 10 XY9 O3 O6 O 0 1 N N N N N N 23.084 3.895 -15.775 0.081 1.205 0.377 O3 XY9 11 XY9 O39 O7 O 0 1 N N N N N N 24.015 2.228 -17.228 1.855 1.778 -1.065 O39 XY9 12 XY9 O40 O8 O 0 1 N N N N N N 23.292 1.544 -15.099 -0.176 2.945 -1.330 O40 XY9 13 XY9 O41 O9 O 0 1 N N N N N N 25.282 2.928 -15.354 0.997 3.357 0.673 O41 XY9 14 XY9 O4 O10 O 0 1 N N N N N N 22.363 5.193 -12.593 2.360 -0.318 -0.440 O4 XY9 15 XY9 O44 O11 O 0 1 N N N N N N 22.273 5.261 -10.142 3.931 -2.098 0.165 O44 XY9 16 XY9 O45 O12 O 0 1 N N N N N N 24.342 5.549 -11.240 4.595 0.163 0.134 O45 XY9 17 XY9 O46 O13 O 0 1 N N N N N N 23.312 3.408 -11.189 2.958 -0.713 1.806 O46 XY9 18 XY9 S33 S1 S 0 1 N N N N N N 18.416 4.471 -15.216 -3.660 0.084 0.420 S33 XY9 19 XY9 S38 S2 S 0 1 N N N N N N 23.994 2.541 -15.830 0.795 2.357 -0.316 S38 XY9 20 XY9 S43 S3 S 0 1 N N N N N N 23.112 4.817 -11.214 3.506 -0.674 0.496 S43 XY9 21 XY9 H2 H1 H 0 1 N N N N N N 20.867 4.399 -16.576 -1.426 -0.893 0.943 H51 XY9 22 XY9 H51 H2 H 0 1 N N N N N N 23.798 6.577 -15.250 0.992 -1.996 -1.963 H6 XY9 23 XY9 H52 H3 H 0 1 N N N N N N 23.444 7.268 -13.630 1.733 -2.923 -0.636 H52 XY9 24 XY9 H1 H4 H 0 1 N N N N N N 20.420 6.924 -16.328 -1.424 -1.743 -1.990 H1 XY9 25 XY9 H3 H6 H 0 1 N N N N N N 21.751 3.405 -14.293 0.006 0.296 -1.479 H3 XY9 26 XY9 H4 H7 H 0 1 N N N N N N 23.961 4.774 -13.769 1.105 -1.160 0.971 H4 XY9 27 XY9 O1 O14 O 0 1 N N N N N N 22.297 6.474 -17.041 -2.658 -2.654 -0.606 O1 XY9 28 XY9 H6 HX H 0 1 N N N N N N 17.192 3.977 -13.780 -4.024 0.806 2.368 H2 XY9 29 XY9 H5 H5 H 0 1 N N N N N N 22.981 0.873 -15.696 0.182 3.691 -1.831 H5 XY9 30 XY9 H7 H9 H 0 1 N N N N N N 22.710 5.956 -9.665 4.661 -2.427 0.708 H7 XY9 31 XY9 HO1 H8 H 0 1 N N N N N N 22.497 7.376 -17.262 -2.776 -3.489 -1.079 H8 XY9 32 # 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 XY9 O39 S38 DOUB N N 1 XY9 O34 S33 DOUB N N 2 XY9 C1 C2 SING N N 3 XY9 C1 O5 SING N N 4 XY9 S38 O3 SING N N 5 XY9 S38 O41 DOUB N N 6 XY9 S38 O40 SING N N 7 XY9 O3 C3 SING N N 8 XY9 C2 O2 SING N N 9 XY9 C2 C3 SING N N 10 XY9 O35 S33 DOUB N N 11 XY9 S33 O2 SING N N 12 XY9 S33 O36 SING N N 13 XY9 O5 C5 SING N N 14 XY9 C3 C4 SING N N 15 XY9 C5 C4 SING N N 16 XY9 C4 O4 SING N N 17 XY9 O4 S43 SING N N 18 XY9 O45 S43 DOUB N N 19 XY9 S43 O46 DOUB N N 20 XY9 S43 O44 SING N N 21 XY9 C2 H2 SING N N 22 XY9 C5 H51 SING N N 23 XY9 C5 H52 SING N N 24 XY9 C1 H1 SING N N 25 XY9 C3 H3 SING N N 26 XY9 C4 H4 SING N N 27 XY9 C1 O1 SING N N 28 XY9 O36 H6 SING N N 29 XY9 O40 H5 SING N N 30 XY9 O44 H7 SING N N 31 XY9 O1 HO1 SING N N 32 # 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 XY9 SMILES ACDLabs 12.01 "OC1OCC(OS(=O)(=O)O)C(OS(=O)(=O)O)C1OS(=O)(=O)O" XY9 InChI InChI 1.06 "InChI=1S/C5H10O14S3/c6-5-4(19-22(13,14)15)3(18-21(10,11)12)2(1-16-5)17-20(7,8)9/h2-6H,1H2,(H,7,8,9)(H,10,11,12)(H,13,14,15)/t2-,3+,4-,5-/m1/s1" XY9 InChIKey InChI 1.06 HTLRKRSDQUPPML-KKQCNMDGSA-N XY9 SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1OC[C@@H](O[S](O)(=O)=O)[C@H](O[S](O)(=O)=O)[C@H]1O[S](O)(=O)=O" XY9 SMILES CACTVS 3.385 "O[CH]1OC[CH](O[S](O)(=O)=O)[CH](O[S](O)(=O)=O)[CH]1O[S](O)(=O)=O" XY9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@H]([C@@H]([C@H]([C@@H](O1)O)OS(=O)(=O)O)OS(=O)(=O)O)OS(=O)(=O)O" XY9 SMILES "OpenEye OEToolkits" 2.0.7 "C1C(C(C(C(O1)O)OS(=O)(=O)O)OS(=O)(=O)O)OS(=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 XY9 "SYSTEMATIC NAME" ACDLabs 12.01 2,3,4-tri-O-sulfo-beta-D-xylopyranose XY9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{R},4~{S},5~{R})-2-oxidanyl-3,5-disulfooxy-oxan-4-yl] hydrogen sulfate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site XY9 "Create component" 2022-08-09 RCSB XY9 "Initial release" 2023-07-12 RCSB XY9 "Other modification" 2023-11-06 RCSB # 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 XY9 "CARBOHYDRATE ANOMER" beta PDB ? XY9 "CARBOHYDRATE ISOMER" D PDB ? XY9 "CARBOHYDRATE RING" pyranose PDB ? XY9 "CARBOHYDRATE PRIMARY CARBONYL GROUP" aldose PDB ? # _pdbx_chem_comp_related.comp_id XY9 _pdbx_chem_comp_related.related_comp_id XYP _pdbx_chem_comp_related.relationship_type "Carbohydrate core" _pdbx_chem_comp_related.details ? # loop_ _pdbx_chem_comp_atom_related.ordinal _pdbx_chem_comp_atom_related.comp_id _pdbx_chem_comp_atom_related.atom_id _pdbx_chem_comp_atom_related.related_comp_id _pdbx_chem_comp_atom_related.related_atom_id _pdbx_chem_comp_atom_related.related_type 1 XY9 C2 XYP C2 "Carbohydrate core" 2 XY9 C5 XYP C5 "Carbohydrate core" 3 XY9 C1 XYP C1 "Carbohydrate core" 4 XY9 C3 XYP C3 "Carbohydrate core" 5 XY9 C4 XYP C4 "Carbohydrate core" 6 XY9 O5 XYP O5 "Carbohydrate core" 7 XY9 O2 XYP O2 "Carbohydrate core" 8 XY9 O3 XYP O3 "Carbohydrate core" 9 XY9 O4 XYP O4 "Carbohydrate core" 10 XY9 H2 XYP H2 "Carbohydrate core" 11 XY9 H51 XYP H51 "Carbohydrate core" 12 XY9 H52 XYP H52 "Carbohydrate core" 13 XY9 H1 XYP H1 "Carbohydrate core" 14 XY9 H3 XYP H3 "Carbohydrate core" 15 XY9 H4 XYP H4 "Carbohydrate core" 16 XY9 O1 XYP O1 "Carbohydrate core" 17 XY9 HO1 XYP HO1 "Carbohydrate core" #