The signal recognition particle protein is a GTPase and is essential for co-translational translocation of innermembrane proteins in E. coli. Since it has a human homologue and highly conserved active site selective inhibition of this protein is difficult to achieve. With the recent computational fragment based method, FTMAP, it is possible to accurately identify alternative drug binding sites on protein surfaces that can be used for screening lead compounds. In this study, we have identified the allosteric druggable sites of signal recognition particle of E. coli using FTMAP. Initial amino acid sequence analysis showed E. coli protein to be 32% identical to human counterpart that includes the four characteristic GTPase motifs and the ‘ALLEADV’ motif. Mapping of crystal structures of E. coli protein revealed six pockets of which two were orthosteric and four were non-orthosteric sites distributed in the inter-domain, protein-protein and solvent interface regions and structurally conserved in T. aquaticus protein. Since these pockets are formed by residues poorly conserved in human protein and present in allosteric space of protein, selective allosteric inhibition is possible, thus qualifying as potential drug target. This study is significant as it reiterates the druggability of prokaryotic essential proteins with human homologues.