The application of a combination of potentiometric, spectrophotometric and nuclear magnetic resonance (NMR) pH titrimetric methodology to measure the macroscopic and to calculate the microscopic protonation constants of SKI-606, a multi-protic compound is described. This compound is currently under evaluation as a candidate drug for the treatment of cancer. SKI-606 was found to have four protonatable sites in the pH range 1–12. Two of these were well separated (Δlog K > 3), whereas the other two overlapped to form a di-protic system. Protonation at only two of the sites yielded a change in the UV spectrum, but the protonation at all four sites could be monitored by NMR. The microscopic equilibrium constants were calculated from the NMR data, which were used in combination with the potentiometric macroscopic constants to calculate the distribution of micro-species.