The heat shock protein 90 (Hsp90) plays an important role in growth and progression of tumor cells through the appropriate folding, conformational maturation and activation of several hundred protein substrates (client proteins). Thus, Hsp90 attracts a great many of interests as a promising target for antitumor drugs which results in more than 20 inhibitors advancing to clinical trials. Here, we designed and synthesized a small molecule inhibitor: FS36 and the X-ray diffraction data of the complex crystal of Hsp90^N-FS36 is collected. High-resolution X-ray crystallography shows that FS36 interacts with Hsp90^N at the ATP-binding pocket and this demonstrates that FS36 possibly substitutes nucleotides to bind to Hsp90^N. The complex crystal structure and the interactions between FS36 and Hsp90^N lay the foundation of the design and majorization of novel antitumor drugs.