P-glycoprotein (Pgp) is a plasma membrane efflux transport. It plays an important role in protecting tissues from toxic xenobiotic which also has the drawback to affect the uptake and distribution of many important drugs. Homology modeling has been a new technique to predicting 3-D structure of a protein not yet confirmed and to complement x-ray crystallography and NMR structure determination. A homology modeling can help to understand Pgp substrate binding, will be advantageous in designing drug delivery process and as well can give an insight of Pgp mechanism. The accuracy of a homology modeling increases with a great yield of template and targeted sequence alignment.  3G60.pbd, a MDR1 template, was collected from Protein Data Bank (PDB) and with our targeted amino acid sequence Pgp gave an 81% alignment similarity between the two. After homology model was generated, we ran a RMSD scan to measure the accuracy between template and targeted sequence. As we further assessment was ran using What If and What Check website to analyze any protein violations.

Homology model of MDR1 (P-glycoprotein)

248th National Meeting (2014)

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