Structure of PDB 5f93 Chain A Binding Site BS02

Receptor Information

>5f93 Chain A (length=424) Species: 210 (Helicobacter pylori)

NYENLSKLLTRYSTLNTLIKLSADPSAINAARENLGASAKNLIGDTKNSP
AYQAVLLAINAAVGFWNVLGYATQCGGNANGQESTSSTTIFNNEPGYRST
SITCSLNRYKPGYYGPMSIENFKKLNEAYQILQTALNKGLPALKENNGTI
KDVTYSYICYGEGNNNCEIKLADGQKLQQNGGSETTTQTIDGKTVSTTIS
SKVVDSTAADNTYKQSYTEITNALKDVPDSAQALLAQASTLINTINTACP
YFSVTNKSGGPQMEPTRGKLCGFTEEISAIQKMITDAQELVNQTSVINEH
EQSTPVGGKPFNPFTDASFAQGMLANASAQAKMLNLAHQVGQTINPDNLT
GTFKNFVTGFLATCNNKGSPPGTVTTQTFASGCAYVEQTITNLNNSIAHF
GTQEQQIQQAENIADTLVNFGSHH

Ligand information

• Ligand ID: FUC
• InChI: InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3+,4+,5-,6+/m0/s1
• InChIKey: SHZGCJCMOBCMKK-SXUWKVJYSA-N
• SMILES:
  CACTVS 3.341: C[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C@@H]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)C
  OpenEye OEToolkits 1.5.0: CC1C(C(C(C(O1)O)O)O)O
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@H]([C@H]([C@@H]([C@@H](O1)O)O)O)O
  CACTVS 3.341: C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
• Formula: C6 H12 O5
• Name: alpha-L-fucopyranose;
  alpha-L-fucose;
  6-deoxy-alpha-L-galactopyranose;
  L-fucose;
  fucose
• ChEMBL: CHEMBL1232862
• DrugBank: DB04473
• ZINC: ZINC000001532814
• PDB chain: 5f93 Chain I Residue 5

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5f93 Structural Insights into Polymorphic ABO Glycan Binding by Helicobacter pylori.
• Resolution: 2.99 Å
• Binding residue (original residue number in PDB): C190 Y191 G192 N195 Q210 Y248 T249
• Binding residue (residue number reindexed from 1): C159 Y160 G161 N164 Q179 Y217 T218
• Annotation score: 4

External links

• PDB: RCSB:5f93, PDBe:5f93, PDBj:5f93
• PDBsum: 5f93
• PubMed: 26764597
• UniProt: O52269;
  Q6DSX7