sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2008-03-18
| Name: | Histone deacetylase 4 |
|---|---|
| ID: | HDAC4_HUMAN |
| AC: | P56524 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.5.1.98 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 62 % |
| B | 38 % |
| B-Factor: | 19.434 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.982 | 1022.625 |
| % Hydrophobic | % Polar |
|---|---|
| 50.83 | 49.17 |
| According to VolSite | |
| HET Code: | TFG |
|---|---|
| Formula: | C19H17F3N3O3S |
| Molecular weight: | 424.417 g/mol |
| DrugBank ID: | DB08613 |
| Buried Surface Area: | 74.84 % |
| Polar Surface area: | 108.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -17.833 | 6.69386 | -11.291 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| C9 | CD1 | LEU- 78 | 3.76 | 0 | Hydrophobic |
| C9 | CE2 | TYR- 79 | 3.92 | 0 | Hydrophobic |
| C17 | CG | PRO- 83 | 3.79 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 121 | 3.89 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 121 | 4.06 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 121 | 3.97 | 0 | Hydrophobic |
| C14 | CB | ALA- 124 | 3.56 | 0 | Hydrophobic |
| F1 | CB | PRO- 156 | 3.66 | 0 | Hydrophobic |
| F2 | CG | PRO- 156 | 3.42 | 0 | Hydrophobic |
| O3 | NE2 | HIS- 158 | 3.1 | 172.42 | H-Bond (Protein Donor) |
| O3 | NE2 | HIS- 159 | 2.78 | 156.22 | H-Bond (Ligand Donor) |
| F2 | CD1 | PHE- 168 | 4.3 | 0 | Hydrophobic |
| F3 | CD1 | PHE- 168 | 3.83 | 0 | Hydrophobic |
| F2 | SG | CYS- 169 | 3.8 | 0 | Hydrophobic |
| C17 | CG | PRO- 298 | 4.48 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 299 | 4.31 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 299 | 3.93 | 0 | Hydrophobic |
| F1 | CB | GLU- 329 | 4.33 | 0 | Hydrophobic |
| O3 | ZN | ZN- 1411 | 2.34 | 0 | Metal Acceptor |
| O2 | ZN | ZN- 1411 | 2.01 | 0 | Metal Acceptor |
