Table 3. Querying PI-PLC using partial motifs derived from the atoms in vildagliptin that make contact to the DPP4 enzyme (PDBid:3W2TA).

The comparison is done using apo enzymes (PDBid:1PTDA for PI-PLC and PDBid:2OQIA for DPP4), since the binding of a ligand induces spatial and electrostatic changes in the active site. The fifth motif has the least rmsd deviation, and comprises of active site residues (involved in the binding of myo-inositol in PDBid:1PTGA). Out of the best matches in the other four motifs, three do not comprise of active site residues (motifs 2, 3 and 4). Motif 1 has a reasonably significant match, and has three residues (Asp67, Asp198 and Trp178) in common with the best match for Motif 5. These three residues from PI-PLC (Asp67, Asp198 and Trp178) and corresponding three residues from DPP4 (Glu205, Glu206 and Tyr662) were used to superimpose DPP4 and PI-PLC. N = Motif number. D = Pairwise distance in Å. PD = Pairwise potential difference. Rmsd = Root mean square deviation. Max = maximum pairwise distance deviation. APBS writes out the electrostatic potential 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	N	Active site atoms(a,b,c,d)		ab	ac	ad	bc	bd	cd	Rmsd/Max (Å)
2OQIA 1PTDA	1	S630OG,E205OE1,Y662CZ,E206OE1 S113OG,D67OD1,W178CZ2,D198OD1	D PD D PD	9.5 237 4.3 195	7.8 -104 6.7 -79	11.2 228 10.1 277	7.2 -341 6.7 -275	6.6 -9 7.7 81	5.8 332 4.9 357	0.9/5.1
2OQIA 1PTDA	2	S630OG,E205OE1,Y662CZ,Y547CZ S244OG,D274OD1,Y275CZ,Y246CZ	D PD D PD	9.5 237 11.3 312	7.8 -104 7.2 -104	5.4 -241 8.1 -171	7.2 341 7.0 -417	11.3 -478 11.6 -484	9.3 -137 5.9 -67	0.8/3.3
2OQIA 1PTDA	3	S630OG,E205OE1,E206OE1,Y547CZ S129OG,D126OD1,E125OE1,Y164CZ	D PD D PD	9.5 237 7.3 172	11.2 228 12.5 262	5.4 -241 6.7 -232	6.6 -9 5.5 90	11.3 -478 12.9 -405	10.4 -469 17.4 -495	1.3/7.0
2OQIA 1PTDA	4	S630OG,Y662CZ,E206OE1,Y547CZ S244OG,Y275CZ,D274OD1,Y246CZ	D PD D PD	7.8 -104 7.2 -104	11.2 228 11.3 312	5.4 -241 8.1 -171	5.8 332 7.0 417	9.3 -137 5.9 -67	10.4 -469 11.6 -484	0.8/3.3
2OQIA 1PTDA	5	E205OE1,Y662CZ,E206OE1,Y547CZ D67OD1,W178CZ2,D198OD1,Y200CZ	D PD D PD	7.2 -341 6.7 -275	6.6 -9 7.7 81	11.3 -478 11.6 -318	5.8 332 4.9 357	9.3 -137 9.6 -42	10.4 -469 6.3 -400	0.7/4.0