sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.150 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 | 36 % |
| B | 64 % |
| B-Factor: | 32.324 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.040 | 2733.750 |
| % Hydrophobic | % Polar |
|---|---|
| 55.06 | 44.94 |
| According to VolSite | |
| HET Code: | TFG |
|---|---|
| Formula: | C19H17F3N3O3S |
| Molecular weight: | 424.417 g/mol |
| DrugBank ID: | DB08613 |
| Buried Surface Area: | 72.54 % |
| 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 |
|---|---|---|
| 25.0138 | -0.589483 | 20.4497 |
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 | CD2 | LEU- 78 | 3.34 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 78 | 3.76 | 0 | Hydrophobic |
| C9 | CE2 | TYR- 79 | 3.97 | 0 | Hydrophobic |
| C16 | CG | PRO- 83 | 3.9 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 121 | 4.18 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 121 | 3.68 | 0 | Hydrophobic |
| C14 | CB | ALA- 124 | 3.69 | 0 | Hydrophobic |
| F2 | CB | PRO- 156 | 3.62 | 0 | Hydrophobic |
| F1 | CG | PRO- 156 | 3.49 | 0 | Hydrophobic |
| O3 | NE2 | HIS- 158 | 3.26 | 156.86 | H-Bond (Protein Donor) |
| O3 | NE2 | HIS- 159 | 2.76 | 155.37 | H-Bond (Ligand Donor) |
| F1 | CD1 | PHE- 168 | 4.06 | 0 | Hydrophobic |
| F3 | SG | CYS- 169 | 3.88 | 0 | Hydrophobic |
| C18 | CG | LEU- 299 | 4.32 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 299 | 3.56 | 0 | Hydrophobic |
| S1 | CD2 | LEU- 299 | 4.45 | 0 | Hydrophobic |
| F2 | CB | GLU- 329 | 4.41 | 0 | Hydrophobic |
| O3 | ZN | ZN- 1410 | 2.28 | 0 | Metal Acceptor |
| O2 | ZN | ZN- 1410 | 2.15 | 0 | Metal Acceptor |
