The Janus kinases (JAKs) are a family of intracellular non-receptor tyrosine kinases which transmit signals by phosphorylation of downstream substrates. A myriad of cytokines can trigger the JAK-STAT pathway which influences immune response, embryonic development, and cellular transformation. Here, we built a comparative model for Jak1 based on the crystal structure of Jak2 (PDB code:2B7A) and Jak3 (PDB code: 1YVJ) using the InsightII package. 3D-Profile and stereochemical analysis further verified the validity of the proposed structure. Adenosine 5'-triphosphate (ATP) was then docked into its catalytic cleft. Although the shape of Jak1 kinase cleft is fairly similar to that of Jak3, we observed minute changes in the key residues of the binding interface which influenced the docking of a specific Jak3 inhibitor, WHI-P131. Superimposition of the interface residues suggested that substitution of Asp 99 (Jak3) into Glu 101 (Jak1) generated steric hindrance and a Tyr 91 to Phe 93 switch altered the shape of catalytic cleft which collectively prohibited the inhibitor binding. Furthermore, in-silico mutagenesis of these two residues back to Asp and Tyr enabled Jak1 to accommodate WHI-P131. These results may provide clues for the design and optimization of selective kinase inhibitors. (c) 2008 Elsevier Inc. All rights reserved.