Structure of PDB 2ydt Chain A Binding Site BS01

Receptor Information

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

GKTFSNVEIFDPPTNYRDPQVLYARPLELSDGTLLGTWENYSPEPPNVWF
PIVKSKDGGKTWKEISKVKDTQNNWGLRYQPQLYELPRAFGKYPKGTVLC
SGSSIPSDLSETLIEVYASRDKGYTWEFVSHVALGGEALPNPGLTPVWEP
FLMTYKEKLILYYSDQRDNATHSQKLVHQTTTDLKKWSKVVDDTKYANYY
ARPGMPTVAKLPNNEYIYVYEYGGGPNPPAGSDYWFPVYYRLSKDPQKFL
NKAHHQIVSNDGTTPAGSPYVVWTPYGGKNGTIVVSCGTRSEIFTNQALG
DASAWKKWDVPQPTAYTRSLLTFQKDPDLLMIMGAGILPPAGGKNTVSAS
VVRLSEVMK

Ligand information

• Ligand ID: EDG
• InChI: InChI=1S/C5H11NO3/c7-2-3-5(9)4(8)1-6-3/h3-9H,1-2H2/t3-,4-,5-/m0/s1
• InChIKey: OQEBIHBLFRADNM-YUPRTTJUSA-N
• SMILES:
  OpenEye OEToolkits 1.6.1: C1[C@@H]([C@H]([C@@H](N1)CO)O)O
  OpenEye OEToolkits 1.6.1: C1C(C(C(N1)CO)O)O
  CACTVS 3.352: OC[C@@H]1NC[C@H](O)[C@H]1O
  CACTVS 3.352: OC[CH]1NC[CH](O)[CH]1O
• Formula: C5 H11 N O3
• Name: 1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL
• ChEMBL: CHEMBL406973
• DrugBank: DB03411
• ZINC: ZINC000001492251
• PDB chain: 2ydt Chain A Residue 500

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): W169 E170 Q195 M226
• Binding residue (residue number reindexed from 1): W148 E149 Q174 M205
• Annotation score: 1
• 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