Based on previous studies on pyridinium derivatives as heat shock protein (hsp90) inhibitors, we explored the pharmacophoric features by measuring the inhibitory effect of synthetic halogenated pyridinium derivatives on hsp90 ATPase site, followed by mapping of the synthetic compounds on successful hypotheses; Hypo1/7 Hypo8/8 and Hypo9/1 previously modelled, then docking of the synthetic compounds on geldanamycin binding site of hsp90 protein 1YET. The inhibition of ATPase activities of hsp90 was measured and expressed as percentage of inhibition for 77 pyridinium derivatives with variable substituent. The highest percentage of inhibition was found for compounds 34, 16 and 48, equal to 48.12% , 42.67% and 40.72% related to 4-bromo-4-flouro-pyridinium derivative , 3-chloro-4-flouro-pyridinium derivative and 4-methylsulfide-4-bromo-pyridnium derivative respectively. Grid based model and 3D QSAR analysis indicate the importance of Van der Waal interaction and electrostatic potential in determining hsp90 inhibition.