A proposed model for the interaction of bisamidine analogues with the B-DNA receptor is established by structure-property relationship studies derived from 3D-WHIM descriptor calculations. Three classes, each with relevant information about structural relationships, were determined by PCA and SIMCA analyses for molecular conformations described by 3D-WHIM descriptors for a set of 29 bisamidines with antileishmaniasis and anti-PCP activities. Shape, distribution and dimension properties mostly govern the interaction of bisamidines with B-DNA through the minor groove AT rich regions.114393397