Structure of PDB 5dts Chain D Binding Site BS01

Receptor Information

>5dts Chain D (length=241) Species: 573 (Klebsiella pneumoniae)

WQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKI
PNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQ
EFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLR
KLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVG
WVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP

Ligand information

• Ligand ID: 5F8
• InChI: InChI=1S/C12H9NO2/c14-12(15)10-4-1-3-9(7-10)11-5-2-6-13-8-11/h1-8H,(H,14,15)
• InChIKey: PXASTGBSGPFLFJ-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: c1cc(cc(c1)C(=O)O)c2cccnc2
  ACDLabs 12.01
  CACTVS 3.385: OC(=O)c1cccc(c1)c2cccnc2
• Formula: C12 H9 N O2
• Name: 3-(pyridin-3-yl)benzoic acid
• ChEMBL: CHEMBL3896367
• ZINC: ZINC000002581037
• PDB chain: 5dts Chain D Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dts Screening and Design of Inhibitor Scaffolds for the Antibiotic Resistance Oxacillinase-48 (OXA-48) through Surface Plasmon Resonance Screening.
• Resolution: 1.94016 Å
• Binding residue (original residue number in PDB): T209 Y211 R250
• Binding residue (residue number reindexed from 1): T185 Y187 R226
• Annotation score: 1
• Binding affinity: MOAD: Kd=280uM
  BindingDB: IC50=240000nM,Kd=280000nM

Enzymatic activity

• Catalytic site (original residue number in PDB): S70 K73 S118 Y123 W157 Y211
• Catalytic site (residue number reindexed from 1): S46 K49 S94 Y99 W133 Y187
• Enzyme Commision number: 3.5.2.6: beta-lactamase.

Gene Ontology

Molecular Function

• GO:0008658 penicillin binding
• GO:0008800 beta-lactamase activity

Biological Process

• GO:0017001 antibiotic catabolic process

External links

• PDB: RCSB:5dts, PDBe:5dts, PDBj:5dts
• PDBsum: 5dts
• PubMed: 27165692
• UniProt: Q6XEC0