ATP-Binding Cassette (ABC) transporters are protein complexes found in all cell types, performing various functions such as multiple drug resistance in eukaryotes and increased pathogenicity in prokaryotes. Polyamines are substances necessary for bacteria in biofilm formation, and cell growth, as well as contributing to the pathogenicity of pathogenic bacteria. The bacterium Enterobacter cloacae, is part of the gastrointestinal tract of humans, however, in other parts of the organism it is pathogenic. The objective of this work was to identify and characterize, through in silico analysis, ABC transporters importing Enterobacter cloacae responsible for the transport of polyamines to identify, through molecular docking, possible strategies of total or partial inhibition of their activities, in search of new therapeutic targets for combating bacterial infection. Two ABC-type polyamine uptake systems were identified in E. cloacae: PotABCD and PotFGHI, whose proteins were identified and characterized. Molecular docking was done for the transporter substrate-binding proteins, showing that the PotF protein is a possible putrescine-binding protein while the PotD protein is possibly a spermidine transporter. Among the analyzes of possible inhibitors, Cystamine and Acetyl-spermine were found, which may be, respectively, possible inhibitors of putrescine and spermidine uptake. The selected ligands have physicochemical characteristics similar to those of the polyamines transported by both periplasmic membranes studied in the present work, namely, Acetylspermine is a synthetic analog inhibitor fused to spermine, and cystamine is a little larger than putrescine and its hydrophobicity is due to the presence of the disulfide bond.