A novel analog of some pyrimidine containing nitrogen based Indole-2-one Schiff’s bases II-4(a-j) were synthesized by n-alkylation/benzylation with substituted Istains and followed by Schiff’s base mechanism with 5-aminopyrimidine-2,4-dione. These synthesized derivatives gave a good yield between 75-86% and all structures were confirmed by FTIR, 1HNMR and Mass spectroscopy. The antibacterial activity of different synthesized nitrogen based indole-2-one Schiff’s bases has been assessed with zone of inhibition by well agar diffusion method, which has shown good activity. Compound II-4f, II-4h and II-4j showed good antibacterial activity against gram positive (Staphylococcus aureus, Bacillus subtilis) and negative bacteria (Escherichia coli, Salmonella paratyphi) with comparison of streptomycin as standard drug. The synthesized molecules were subjected to Molecular docking studies with AUTODOCK VINA suite of MGL tools by using Fgb1 receptor with PDB ID: 3K4P and the compound II-4f (-9.3), II-4h (-9.3) and II-4j(-9.2) were reported highest docking ligands.The docking score of the ligands ranged from -7.2 (compound II-4d) to -9.2(Compound II-4f).