The Pleiotropic Drug Resistance (PDR) network is central to the drug response in fungi, and its overactivation is associated with drug resistance. However, gene regulation of the PDR network is not well understood. Here, we established a method to identify proteins that bind promoter of the PDR5 multidrug transporter gene in Saccharomyces cerevisiae using minichromosome isolation and SILAC-based quantitative proteomics, and identified the SWI/SNF chromatin remodelling complex as a PDR5 promoter-binding complex. We also purified the SWI/SNF complex from S. cerevisiae by immunoprecipitating Flag-tagged Snf6, a subunit of SWI/SNF, and identified the subunits of SWI/SNF and its binding proteins by LC-MS/MS.