I'm not sure if this answer applies to 15N HMQC experiments, but in the past when we did 2-D NMR experiments to measure ligand binding to a protein by measuring chemical shift changes of peaks, a loss of multiple peak intensities was taken to mean that the ligand was binding in a non-specific manner, such as an aggregator or denaturant. Such compounds were discarded.

Adam B Shapiro thanks for the reply.

I've read somewhere that fast exchanges of ligand between the bound and free form results into collapse of two signals into a single peak, as the life time is too short for the observation of individual signals on the NMR time scale.

Could it be the case here?

I should mention that most of the peaks linewidths also show observable broadening.

Sorry if my question is too basic. I'm a real beginner in NMR.

Sorry, I don't know enough about NMR to answer.