Ionotropic glutamate receptors belong to the superfamily of P-loop channels as well as K(+), Na(+), and Ca(2+) channels. However, the structural similarity between ion channels of the glutamate receptors and K(+) channels is a matter of discussion. The aim of this study was to analyze differences between the structures of K(+) channels and glutamate receptor channels. For this purpose, homology models of NMDA and AMPA receptor channels (M2 and M3 segments) were built using X-ray structures of K(+) channels as templates. The models were optimized and used to reproduce specific data on the structure of glutamate receptor channels. Particular attention was paid to the data of the binding of channel blockers and to the results of scanning mutagenesis. The modeling demonstrates that properties of glutamate receptor channel can be reproduced assuming only local structural deformations of the K(+) channel templates. The most valuable differences were found in the selectivity-filter region, whereas helical parts of M2 and M3 segments could have similar spatial organization with homologous segments in K(+) channels. It is concluded that the current experimental data on glutamate receptor channels does not reveal global structural differences with K(+) channels.