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" 
# 
