The efficient structural determination of protein-ligand complexes using NMR and/or X-ray is determined by the affinity of the interaction and the stability of the complex. In order to facilitate the analysis of protein domains bound to peptide ligands, we thought to stabilize the complex using an intermolecular crosslinking approach. As a model complex we have used the WW domain of Nedd4L bound to a short peptide ligand containing the canonical PPxY site. Nedd4L is a HECT-type E3 ubiquitin ligase that regulates the internalization and degradation of a variety of ion channels, membrane receptors and signaling proteins. It also participates in the cross-ubiquitination of ubiquitin ligases, labeling them for degradation. Nedd4L is a modular protein, which contains a C2, four WW and the catalytic HECT domains. The recognition of targets is achieved through interactions of the WW domains and PPxY motifs present in the interacting partners. One of its targets is embedded in the HECT domain that is exposed when the protein is damaged or partially unfolded. Using the structural information provided by the complex structure of the WW3 of Need4L and the PPxY peptide of the HECT domain, we have introduced a cysteine residue in two suitable positions of the WW3 domain via site-directed mutagenesis. Furthermore, we have synthesized an Nα -Fmoc-L-fluoroacetyl lysine (Fmoc-FAcK) building block in a straight forward three step chemical reaction starting from an Nα -tert-butyloxycarbonyl (Boc)-L-lysine. FAcK was incorporated in a synthetic fragment including the PY site via solid phase peptide synthesis. After optimization of the conditions the relatively inert fluoroacetamide of FAcK reacted with the thiol of the cysteine in proximity created by the PY peptide-WW3 protein native contacts.