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 whether endogenous H₂S production and HDAC6 loss are associated with changes in global protein abundance, proteomic profiling was performed in EA.hy926 cells with knockout of cystathionine γ-lyase (CSE, encoded by CTH) or HDAC6. This dataset contains the proteomics data comparing CSE-knockout versus wild-type cells and HDAC6-knockout versus wild-type cells.