Structure of PDB 2ydt Chain A Binding Site BS02

Receptor Information

>2ydt Chain A (length=359) Species: 5518 (Fusarium graminearum)

GKTFSNVEIFDPPTNYRDPQVLYARPLELSDGTLLGTWENYSPEPPNVWF
PIVKSKDGGKTWKEISKVKDTQNNWGLRYQPQLYELPRAFGKYPKGTVLC
SGSSIPSDLSETLIEVYASRDKGYTWEFVSHVALGGEALPNPGLTPVWEP
FLMTYKEKLILYYSDQRDNATHSQKLVHQTTTDLKKWSKVVDDTKYANYY
ARPGMPTVAKLPNNEYIYVYEYGGGPNPPAGSDYWFPVYYRLSKDPQKFL
NKAHHQIVSNDGTTPAGSPYVVWTPYGGKNGTIVVSCGTRSEIFTNQALG
DASAWKKWDVPQPTAYTRSLLTFQKDPDLLMIMGAGILPPAGGKNTVSAS
VVRLSEVMK

Ligand information

• Ligand ID: AHR
• InChI: InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4+,5+/m0/s1
• InChIKey: HMFHBZSHGGEWLO-QMKXCQHVSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C([C@H]1[C@@H]([C@H]([C@@H](O1)O)O)O)O
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(O1)O)O)O)O
  CACTVS 3.341: OC[CH]1O[CH](O)[CH](O)[CH]1O
  CACTVS 3.341: OC[C@@H]1O[C@@H](O)[C@H](O)[C@H]1O
  ACDLabs 10.04: OC1C(OC(O)C1O)CO
• Formula: C5 H10 O5
• Name: alpha-L-arabinofuranose;
  alpha-L-arabinose;
  L-arabinose;
  arabinose
• DrugBank: DB03142
• ZINC: ZINC000002569310
• PDB chain: 2ydt Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ydt Alpha-L-Arabinofuranosylated Pyrrolidines as Arabinanase Inhibitors.
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): E60 Q101
• Binding residue (residue number reindexed from 1): E39 Q80
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=5.52,Ki=3.0uM

Enzymatic activity

• Enzyme Commision number: 3.2.1.55: non-reducing end alpha-L-arabinofuranosidase.

Gene Ontology

Molecular Function

• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0046556 alpha-L-arabinofuranosidase activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:2ydt, PDBe:2ydt, PDBj:2ydt
• PDBsum: 2ydt
• PubMed: 21773614
• UniProt: B8ZY56