Table 1 Protein–ligand interaction profiles of vorinostat (SAHA, SHH) and panobinostat with HDAC2, HDAC6, HDAC7, HDAC8, HDACs homolog, and LTA4H.
PDB ID | Hydrogen bond | Hydrophobic Interactions | Metal interactions | Salt bridges | Water bridges |
|---|---|---|---|---|---|
Vorinostat (SAHA, SHH) | |||||
4LXZ (HDAC2) Homo sapiens | Asp104 (2.0/165.67) Tyr308 (1.58/160.71) | Phe155 Phe210 | Asp181(2.00) His183 (2.07) Asp269 (1.90) | SHH-W-Gln265 SHH-W-Tyr308 | |
4QA0 (HDAC8) Homo sapiens | Tyr306 (1.65/163.09) | Phe152,Phe208, Pro273, Tyr306 | Asp178 (1.90) His180 (2.16) Asp267 (2.08) | Asp178 Asp267 | SHH-W-Asp101 |
4QA2 (HDAC8) Homo sapiens | Tyr306 (1.62/170.79) | Phe152,Phe208, Pro273, Tyr306 | Asp178 (2.00) His180 (2.07) Asp267 (2.07) | ||
4BZ6 (HDAC8) Schistosoma mansoni | His292 (2.77/148.04) | Phe216,Pro291, Tyr341 | Asp186 (2.06) His188 (2.12) Asp285 (1.97) | SHH-W-Lys20 SHH-W-Tyr341 | |
3C0Z (HDAC7) Homo sapiens | His670 (1.76/134.23) | Phe679, Phe738 | Asp707 (2.05) His709 (2.03) Asp801 (2.04) | SHH-W-Gly842 | |
1C3S (HDAC homolog) Aquifex aeolicus | Pro22, Phe111 | Asp168 (1.93) His170 (2.16) Asp258 (1.91) | Asp168 Asp258 | ||
1ZZ1 (HDAC like) Alcaligenaceae bacterium FB188 | Asp98 (3.14/109.01) Gly151 (3.37/123.23) | Leu21, Ile100, Phe152, Phe208, Phe341 | Asp180 (2.14) His182 (2.16) Asp268 (1.97) | Asp180 Asp268 | |
4R7L (Leukotriene A4 Hydrolase) Homo sapiens | Gln136 (2.76/105.31) π-stacking_Phe314 | Gln136,Tyr267, Trp311,Phe314, Leu369, Pro374 Tyr378 | His299 (2.07) Glu318 (2.93) | SHH-W-Pro374 SHH-W-Asp375 | |
5EEI (HDAC6) Danio rerio | His573 (2.49/167.65) His574 (1.91/140.31) Tyr745 (1.74/174.81) | Pro464,Phe583, Phe643,Leu712 | Asp612 His614 Asp705 | ||
1T69 (HDAC8) Homo sapiens | His180 (3.41/127.87) | Tyr100,Phe152, Phe208 | Asp178 (2.78) His180 (1.79) Asp267 (1.91) | Asp178 Asp267 | |
Panobinostat (LBH) | |||||
5EF8 (HDAC6) Danio rerio | π-stacking_Phe643 π-cation_His463 | Phe583, Leu712 | Asp612 (2.09) His614 (2.19) Asp705 (1.95) | ||
