Origin of high pathogenicity of an emerging avian influenza H5N1 due to the -RRRKK- insertion at the cleavage loop of the hemagglutinin H5, was studied using the molecular dynamics technique, in comparison with those of the non-inserted H5 and H3 bound to furin active site. The cleavage loop of the highly pathogenic H5 was found to bind strongly to the furin cavity, serving as a conformation suitable for the proteolytic reaction. With this configuration, the appropriate interatomic distances were found for all three reaction centers of the enzyme-substrate complex: there are the arrangement of the catalytic triad, attachment of the catalytic Ser368 to the reactive S1-Arg, and formation of the oxyanion hole. Experimentally, the -RRRKK- insertion was also found to increase in cleavage of hemagglutinin by furin. The simulated data provide a clear answer to the question of why inserted H5 is better cleaved by furin than the other subtypes, explaining the high pathogenicity of avian influenza H5N1.