Histone deacetylase 6 (HDAC6) is a zinc-dependent hydrolase that plays a critical role in numerous (patho)physiological processes and thus serves as a target of therapeutic interventions in cancers, and neurological and inflammatory diseases. Many HDAC6-specific inhibitors exist that are used as research reagents or are in clinical trials, yet these might have limited specificity and suboptimal pharmacokinetics that is translated into suboptimal therapeutic efficacy. Mahboobi group recently reported Marbostat-100 as a highly selective and potent HDAC6 inhibitor [1] built on the Tubastain A (TubA) scaffold [2]. However, pre-clinical in vivo studies indicated limited plasma stability as its major liability. To assist further development of Marbostat-100, we solved a crystal structure of HDAC6 in a complex with SS-294, a Marbostat-100 derivative with improved pharmacokinetic properties. Our data detail structural features of SS-294 that are critical for efficient interactions with the enzyme and the can be further optimized for improved potency, stability, and selectivity.