Structure of PDB 5qaf Chain A Binding Site BS01

Receptor Information

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

EWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFK
IPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVY
QEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFL
RKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWV
GWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP

Ligand information

• Ligand ID: S1D
• InChI: InChI=1S/C13H9FO2/c14-12-6-4-9(5-7-12)10-2-1-3-11(8-10)13(15)16/h1-8H,(H,15,16)
• InChIKey: YUQPLNXKGVRIAJ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: OC(=O)c1cccc(c1)c2ccc(F)cc2
  OpenEye OEToolkits 2.0.6: c1cc(cc(c1)C(=O)O)c2ccc(cc2)F
• Formula: C13 H9 F O2
• Name: 3-(4-fluorophenyl)benzoic acid
• ChEMBL: CHEMBL121838
• ZINC: ZINC000002565543
• PDB chain: 5qaf Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5qaf A focused fragment library targeting the antibiotic resistance enzyme - Oxacillinase-48: Synthesis, structural evaluation and inhibitor design.
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): T209 R250
• Binding residue (residue number reindexed from 1): T186 R227
• Annotation score: 1
• Binding affinity: MOAD: Kd=312uM
  PDBbind-CN: -logKd/Ki=3.51,Kd=312uM

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:5qaf, PDBe:5qaf, PDBj:5qaf
• PDBsum: 5qaf
• PubMed: 29348071
• UniProt: Q6XEC0