Structure of PDB 5qb0 Chain D Binding Site BS02

Receptor Information

>5qb0 Chain D (length=242) Species: 573 (Klebsiella pneumoniae)

EWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFK
IPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVY
QEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFL
RKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWV
GWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP

Ligand information

• Ligand ID: AVA
• InChI: InChI=1S/C12H9NO2/c14-12(15)10-5-3-4-9(8-10)11-6-1-2-7-13-11/h1-8H,(H,14,15)
• InChIKey: IRXFQXMHMRTLIR-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: c1ccnc(c1)c2cccc(c2)C(=O)O
  CACTVS 3.385: OC(=O)c1cccc(c1)c2ccccn2
• Formula: C12 H9 N O2
• Name: 3-pyridin-2-ylbenzoic acid
• ChEMBL: CHEMBL4172180
• ZINC: ZINC000002563821
• PDB chain: 5qb0 Chain D Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5qb0 A focused fragment library targeting the antibiotic resistance enzyme - Oxacillinase-48: Synthesis, structural evaluation and inhibitor design.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): T104 Y117 T209 R250
• Binding residue (residue number reindexed from 1): T81 Y94 T186 R227
• Annotation score: 1
• Binding affinity: MOAD: Kd=159uM

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:5qb0, PDBe:5qb0, PDBj:5qb0
• PDBsum: 5qb0
• PubMed: 29348071
• UniProt: Q6XEC0