Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach

Methods Enzymol. 2011;493:241-75. doi: 10.1016/B978-0-12-381274-2.00010-8.


Over the last 15 years, the role of NMR spectroscopy in the lead identification and optimization stages of pharmaceutical drug discovery has steadily increased. NMR occupies a unique niche in the biophysical analysis of drug-like compounds because of its ability to identify binding sites, affinities, and ligand poses at the level of individual amino acids without necessarily solving the structure of the protein-ligand complex. However, it can also provide structures of flexible proteins and low-affinity (K(d)>10(-6)M) complexes, which often fail to crystallize. This chapter emphasizes a throughput-focused protocol that aims to identify practical aspects of binding site characterization, automated and semiautomated NMR assignment methods, and structure determination of protein-ligand complexes by NMR.

MeSH terms

  • Automation, Laboratory
  • Binding Sites*
  • Drug Design
  • Drug Discovery / methods*
  • Hydrogen Bonding
  • Ligands
  • Magnetic Resonance Spectroscopy / methods*
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular / methods
  • Proteins / chemistry*
  • Software


  • Ligands
  • Proteins