Hydrogen sulfide (H₂S) is an endogenous gasotransmitter implicated in the regulation of protein function. This study investigates whether H₂S-derived sulfur species can engage the catalytic Zn²⁺ center of histone deacetylase 6 (HDAC6) and influence HDAC6-dependent deacetylation. Molecular dynamics simulations support accessibility of HS⁻ to the HDAC6 CD2 active-site tunnel, whereas biochemical, biophysical and quantum-chemical analyses support a zinc-dependent interaction and the chemical feasibility of Zn–sulfur coordination. To investigate changes in protein acetylation associated with exogenous H₂S exposure, acetylomic profiling was performed in EA.hy926 cells treated with 60 μM NaHS or vehicle. This dataset contains the acetylomics data comparing NaHS-treated cells with vehicle-treated controls.