The small molecule binding to the c-Jun N-terminal kinase 3 (JNK3) was examined by the measurements of saturation transfer difference (STD) NMR experiments. The STD NMR experiment of ATP added to JNK3 clearly showed the binding of the nucleotide to the kinase. The STD NMR spectrum of dNTPs added to JNK3 discriminated the kinase-bound nucleotide from the unbound ones. After the five-fold addition of ATP to the dNTPs and JNK3 mixture, only signals of the cognate substrate of JNK3, ATP, were observed from the STD NMR experiment. These results signify that by the STD NMR the small molecules bound to JNK3 can be discriminated from the pool of the unbound molecules. Furthermore the binding mode of the small molecule to JNK3 can be determined by the competition experiments with ATP.