Structure of PDB 5qa9 Chain B Binding Site BS01

Receptor Information

>5qa9 Chain B (length=242) Species: 573 (Klebsiella pneumoniae)

EWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFK
IPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVY
QEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFL
RKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWV
GWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP

Ligand information

• Ligand ID: QKU
• InChI: InChI=1S/C14H12O3/c15-9-10-3-1-4-11(7-10)12-5-2-6-13(8-12)14(16)17/h1-8,15H,9H2,(H,16,17)
• InChIKey: SWVDMIKPVOEKNC-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: OCc1cccc(c1)c2cccc(c2)C(O)=O
  OpenEye OEToolkits 2.0.6: c1cc(cc(c1)c2cccc(c2)C(=O)O)CO
• Formula: C14 H12 O3
• Name: 3-[3-(hydroxymethyl)phenyl]benzoic acid
• ChEMBL: CHEMBL4172334
• ZINC: ZINC000016947602
• PDB chain: 5qa9 Chain B Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5qa9 A focused fragment library targeting the antibiotic resistance enzyme - Oxacillinase-48: Synthesis, structural evaluation and inhibitor design.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): D101 Y211 R250
• Binding residue (residue number reindexed from 1): D78 Y188 R227
• Annotation score: 1
• Binding affinity: MOAD: Kd=230uM

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:5qa9, PDBe:5qa9, PDBj:5qa9
• PDBsum: 5qa9
• PubMed: 29348071
• UniProt: Q6XEC0