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Schizencephaly (SCH) is congenital brain malformation whose hallmark is the presence of one or more cleft spanning the pial surface and ependymal of one or both cerebral hemispheres associated with Homeobox protein EMX2. In current study, hybrid approach of comparative modeling and molecular docking were followed. An inhibitor (C12H15N3O2S) scrutinized from PubChem showed maximum binding affinity against EMX2. Docking studies revealed that Asn-66, Phe-71, Ala-72, Glu-73, Leu-108, Phe-109, Ala-110, Ser-111, Gln-112, Gln-113 and Tyr-127 are critical residues for receptor-ligand interaction. Comparative modeling approach coupled with docking energies and drug likeness rules illustrated that selected inhibitor protein kinase are potential inhibitor compound for targeting EMX2. This study suggests that selected inhibitor might be potent molecule based on the binding energy values and drug score. Further analysis of this inhibitor could be helpful for exploring the details of binding sites. Overall, findings of current effort may be helpful in designing the novel therapeutic targets to cure SCH.