Pd-SNBD enables fluorogenic, selective, and stable labeling of peptides. Benzodiazole fluorophores can be synthesized with variable bridging groups (e.g., oxygen, sulfur, selenium), therefore we first investigated the effect of different heteroatoms in the fluorogenic behavior of Cys-ligated constructs. We synthetized three Cys-benzodiazole amino acids including O-bridged, S-bridged and Se-bridged fluorophores, and measured their fluorescence properties in mixtures of dioxane:water, mimicking both hydrophilic and hydrophobic microenvironments. All three amino acids showed notable fluorogenic behavior (from 6-fold to 27-fold fluorescence increases, Figure ) with Cys-SNBD showing the lowest background signals in water and the strongest fluorescence response in hydrophobic conditions. The environmental sensitivity of Cys-SNBD was further corroborated by measuring the fluorescence emission in solvents with variable polarity (Figure ), thus confirming the suitability of the S-bridged benzodiazole to build some of the first Pd-based fluorogenic reagents for late-stage incorporation in intact peptides and proteins (Figure ). Encouraged by these results, we designed our labeling strategy by preparing one Pd-OAC bearing the Sbridged benzodiazole group that would be suitable for reacting with Cys residues. For this purpose, we synthesized the brominated analogue SNBD-Br (Figure ) and coupled it to the complex [(COD)Pd(CH2TMS)2] in the presence of a RuPhos ligand to isolate (72% yield) and characterize the crystal structure of the desired Pd-SNBD complex (Figures and; see synthetic and full characterization details in Supporting Information). Notably, the synthesis of Pd-SNBD was scalable to 50 milligrams and stability studies proved that the reagent was stable and reactive after storage under nitrogen atmosphere and room temperature for several months (Figure ).