Structure of PDB 5qaw Chain D Binding Site BS01

Receptor Information

>5qaw Chain D (length=242) Species: 573 (Klebsiella pneumoniae)

EWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFK
IPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVY
QEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFL
RKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWV
GWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP

Ligand information

• Ligand ID: TVC
• InChI: InChI=1S/C17H12O2/c18-17(19)16-7-3-6-14(11-16)15-9-8-12-4-1-2-5-13(12)10-15/h1-11H,(H,18,19)
• InChIKey: QOPDOKREBSOVNG-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: OC(=O)c1cccc(c1)c2ccc3ccccc3c2
  OpenEye OEToolkits 2.0.6: c1ccc2cc(ccc2c1)c3cccc(c3)C(=O)O
• Formula: C17 H12 O2
• Name: 3-naphthalen-2-ylbenzoic acid
• ChEMBL: CHEMBL4159328
• ZINC: ZINC000002529015
• PDB chain: 5qaw Chain D Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5qaw A focused fragment library targeting the antibiotic resistance enzyme - Oxacillinase-48: Synthesis, structural evaluation and inhibitor design.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): S70 S118 T209 G210 Y211 S244 R250
• Binding residue (residue number reindexed from 1): S47 S95 T186 G187 Y188 S221 R227
• Annotation score: 1
• Binding affinity: MOAD: Kd=400uM

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