Structure of PDB 5qad Chain A Binding Site BS01

Receptor Information

>5qad Chain A (length=242) Species: 573 (Klebsiella pneumoniae)

EWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFK
IPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVY
QEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFL
RKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWV
GWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP

Ligand information

• Ligand ID: WVV
• InChI: InChI=1S/C13H9FO2/c14-12-7-2-1-6-11(12)9-4-3-5-10(8-9)13(15)16/h1-8H,(H,15,16)
• InChIKey: KJRAPRROUUCCPO-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: c1ccc(c(c1)c2cccc(c2)C(=O)O)F
  CACTVS 3.385: OC(=O)c1cccc(c1)c2ccccc2F
• Formula: C13 H9 F O2
• Name: 3-(2-fluorophenyl)benzoic acid
• ChEMBL: CHEMBL122977
• ZINC: ZINC000002574076
• PDB chain: 5qad Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5qad A focused fragment library targeting the antibiotic resistance enzyme - Oxacillinase-48: Synthesis, structural evaluation and inhibitor design.
• Resolution: 1.75 Å
• Binding residue (original residue number in PDB): Y211 R250
• Binding residue (residue number reindexed from 1): Y188 R227
• Annotation score: 1
• Binding affinity: MOAD: Kd=170uM
  PDBbind-CN: -logKd/Ki=3.77,Kd=170uM

Enzymatic activity

• Catalytic site (original residue number in PDB): S70 K73 S118 Y123 W157 Y211
• Catalytic site (residue number reindexed from 1): S47 K50 S95 Y100 W134 Y188
• Enzyme Commision number: 3.5.2.6: beta-lactamase.

Gene Ontology

Molecular Function

• GO:0008658 penicillin binding
• GO:0008800 beta-lactamase activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0017001 antibiotic catabolic process
• GO:0046677 response to antibiotic
• GO:0071555 cell wall organization

External links

• PDB: RCSB:5qad, PDBe:5qad, PDBj:5qad
• PDBsum: 5qad
• PubMed: 29348071
• UniProt: Q6XEC0