The influenza virus hemagglutinin is a potential drug target for antivirus 
treatment. A variety of membrane fusion inhibitors targeting hemagglutinin have 
been discovered, but the binding sites and modes, important for understanding 
membrane fusion and rational drug design, have not yet been elucidated. In this 
article, we investigated the possible hemagglutinin binding sites for the 
current membrane fusion inhibitors. Four possible binding pockets (Pocket A, B, 
C, and D) at the stalk region of hemagglutinin were detected and defined using 
the CAVITY program. Most of the current membrane fusion inhibitors were reported 
to bind to Pocket C by amino acid mutation experiments and molecular modeling 
simulation. However, our binding site prediction suggested that Pocket A is the 
best ligand binding site other than Pocket C. Using a specific computational 
protocol combining molecular docking, three-dimensional QSAR, and receptor 
mimicking, we further found that Pocket A is the putative binding site for a 
series of membrane fusion inhibitors (1-phenyl-cycloalkane carbamides). This is 
further proven by the antiviral spectrum of the inhibitors. This protocol for 
the identification of ligand binding sites in influenza hemagglutinin is also 
applicable for the analysis of other protein targets with no explicit binding 
information.