Table 6. Potential and spatial congruence of the residues binding vildagliptin in DPP4 structure (PDBid:2OQIA) to the putative binding site in PI-PLC structure (PDBid:1PTDA).
Both the structures are apo enzymes, since the binding of a ligand induces spatial and electrostatic changes in the active site. Ser630 in DPP4 has a significant spatial difference as compared to Ser234 in PI-PLC (pair ‘bc’ has a difference of 5 Å), and also a reasonable electrostatic difference (pair ‘ac’ has a difference of 144 PD units). D = Pairwise distance in Å. PD = Pairwise potential difference. 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 | Active site atoms(a,b,c,d) | ab | ac | ad | bc | bd | cd | |
|---|---|---|---|---|---|---|---|---|
| 2OQIA
|
GLU205OE1,GLU206OE2,SER630OG,TYR662CZ,
|
D
PD |
5.2
31.7 |
9.5
-237.4 |
7.2
-341.5 |
10.1
-269.1 |
4.2
-373.2 |
7.8
-104.1 |
| 1PTDA
|
ASP67OD1,ASP198OD1,SER234OG,TRP178CZ2,
|
D
PD |
7.7
81.8 |
8.2
-93.7 |
6.7
-275.7 |
5.7
-175.6 |
4.9
-357.6 |
9.2
-182.0 |