NMR-Based Determination of the 3D Structure of the Ligand–Protein Interaction Site without Protein Resonance Assignment

Molecular replacement in X-ray crystallography
is the prime method
for establishing structure–activity relationships of pharmaceutically
relevant molecules. Such an approach is not available for NMR. Here,
we establish a comparable method, called NMR molecular replacement
(NMR2). The method requires experimentally
measured ligand intramolecular NOEs and ligand–protein intermolecular
NOEs as well as a previously known receptor structure or model. Our
findings demonstrate that NMR2 may open
a new avenue for the fast and robust determination of the interaction
site of ligand–protein complexes at atomic resolution.