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

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

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Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.


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.

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