Van der Waals (vdW) interaction, and its subtle interplay with chemically specific interactions and surface roughness at metal/organic interfaces, is critical to the understanding of structure-function relations in diverse areas, including catalysis, molecular electronics and self-assembly(1-3). However, vdW interactions remain challenging to characterize directly at the fundamental, single-molecule level both in experiments and in first principles calculations with accurate treatment of the non-local, London dispersion interactions. In particular, for metal/organic interfaces, efforts so far have largely focused on model systems consisting of adsorbed molecules on flat metallic surfaces with minimal specific chemical interaction(4-9). Here we show, through measurements of single-molecule mechanics, that pyridine derivatives(10,11) can bind to nanostructured Au electrodes through an additional binding mechanism beyond the chemically specific N-Au donor-acceptor bond. Using density functional theory simulations we show that vdW interactions between the pyridine ring and Au electrodes can play a key role in the junction mechanics. These measurements thus provide a quantitative characterization of vdW interactions at metal/organic interfaces at the single-molecule level.