Table 2. Changes in the conformation of the binding site due to vildagliptin (a DPP4 inhibitor) binding.

We compare the pairwise distance and electrostatic potential difference (EPD) changes in the apo (PDBid:2OQIA) and holo (PDBid:3W2TA) enzymes. Note that the pairwise distance between these atoms change in the ligand free PDB (2OQIA) as compared to the protein with bound inhibitor (2BUBA). For example, the distance between E205OE2 and E206OE2 (pair ab) changes from 3.9 Å to 5.6 Å. Also, there is a definite change in the EPD between E205OE2 and E205OE2 (pair ab). D = Pairwise distance in Å. PD = Pairwise potential difference. The electrostatic potential are in dimensionless units of kT/e where k is Boltzmann’s constant, T is the temperature in K and e is the charge of an electron.

PDB	Active site atoms (a,b,c,d)		ab	ac	ad	bc	bd	cd
2OQIA apo 3W2TA holo	GLU205OE2,GLU206OE2,SER630OG,TYR662OH, GLU205OE2,GLU206OE2,SER630OG,TYR662OH,	D PD D PD	3.9 75.7 5.6 -74.4	7.9 -193.4 9.1 -307.9	4.0 -94.5 6.1 -159.8	10.1 -269.1 9.4 -233.5	3.5 -170.2 5.1 -85.5	7.3 98.9 5.6 148.1