Structure of PDB 5dtk Chain D Binding Site BS01

Receptor Information

>5dtk Chain D (length=243) Species: 573 (Klebsiella pneumoniae)

KEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTF
KIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPV
YQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISF
LRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWW
VGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP

Ligand information

• Ligand ID: 5F3
• InChI: InChI=1S/C17H12N2O2/c20-17(21)16-10-14(12-1-5-18-6-2-12)9-15(11-16)13-3-7-19-8-4-13/h1-11H,(H,20,21)
• InChIKey: NNTKTJCJOPINGZ-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: C(=O)(O)c2cc(c1ccncc1)cc(c2)c3ccncc3
  OpenEye OEToolkits 1.9.2: c1cnccc1c2cc(cc(c2)C(=O)O)c3ccncc3
  CACTVS 3.385: OC(=O)c1cc(cc(c1)c2ccncc2)c3ccncc3
• Formula: C17 H12 N2 O2
• Name: 3,5-di(pyridin-4-yl)benzoic acid
• ChEMBL: CHEMBL3910343
• PDB chain: 5dtk Chain D Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dtk Screening and Design of Inhibitor Scaffolds for the Antibiotic Resistance Oxacillinase-48 (OXA-48) through Surface Plasmon Resonance Screening.
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): S70 V120 Y211 R250
• Binding residue (residue number reindexed from 1): S48 V98 Y189 R228
• Annotation score: 1
• Binding affinity: MOAD: Kd=50uM
  BindingDB: Kd=50000nM,IC50=18000nM

Enzymatic activity

• Catalytic site (original residue number in PDB): S70 K73 S118 Y123 W157 Y211
• Catalytic site (residue number reindexed from 1): S48 K51 S96 Y101 W135 Y189
• 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:5dtk, PDBe:5dtk, PDBj:5dtk
• PDBsum: 5dtk
• PubMed: 27165692
• UniProt: Q6XEC0