Mechanism of inhibition of glutamine synthetase (EC 6.3.1.2; GS) by phosphinothricin and its analogues was studied in some detail using molecular modeling methods. Among three possible conformations of phosphinothricin in the active site of GS, this compatible with binding mode of methionine sulfoximine, determined recently by crystallography, was found to be energetically favored. Basing on these results eleven inhibitors of GS were docked into its active site. Taking into consideration that phosphinothricin acts as suicide inhibitor, which is due to phosphorylation by the enzyme, seven of studied analogues were additionally analyzed in their phosphorylated forms. All the inhibitor-enzyme complexes were evaluated quantitatively by using eight scoring functions implemented in Insight and Sybyl program packages and significant correlation between the obtained scores and experimental pK(i) values was achieved. Computed surface charge distribution for five selected inhibitors in both free and phosphorylated forms and their comparison with electronic structure of enzymatic reaction transition state allowed us to determine important electronic features required to construct potent inhibitors of glutamine synthetase.