sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.920 Å
X-ray
2014-05-02
| Name: | Histone deacetylase 8 |
|---|---|
| ID: | HDAC8_HUMAN |
| AC: | Q9BY41 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.5.1.98 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 26 % |
| D | 74 % |
| B-Factor: | 23.430 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.393 | 2139.750 |
| % Hydrophobic | % Polar |
|---|---|
| 51.26 | 48.74 |
| According to VolSite | |
| HET Code: | B3N |
|---|---|
| Formula: | C16H25N3O3 |
| Molecular weight: | 307.388 g/mol |
| DrugBank ID: | DB02565 |
| Buried Surface Area: | 65.51 % |
| Polar Surface area: | 81.67 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 4.25532 | 11.105 | 73.8281 |
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 |
| C22 | CZ | TYR- 100 | 4.24 | 0 | Hydrophobic |
| O4 | NE2 | HIS- 142 | 2.53 | 155.18 | H-Bond (Protein Donor) |
| N3 | NE2 | HIS- 143 | 2.76 | 137.49 | H-Bond (Ligand Donor) |
| C21 | CE1 | PHE- 152 | 3.67 | 0 | Hydrophobic |
| C8 | CZ | PHE- 152 | 3.71 | 0 | Hydrophobic |
| C5 | CD1 | PHE- 152 | 3.72 | 0 | Hydrophobic |
| C9 | CG | PHE- 208 | 3.65 | 0 | Hydrophobic |
| C8 | CD1 | PHE- 208 | 4.42 | 0 | Hydrophobic |
| C7 | CE1 | PHE- 208 | 3.98 | 0 | Hydrophobic |
| C6 | CD1 | PHE- 208 | 4.36 | 0 | Hydrophobic |
| C18 | CG | PRO- 273 | 4.49 | 0 | Hydrophobic |
| C14 | CB | PRO- 273 | 3.43 | 0 | Hydrophobic |
| C15 | CG | PRO- 273 | 3.85 | 0 | Hydrophobic |
| C21 | CE | MET- 274 | 4.02 | 0 | Hydrophobic |
| C22 | CD2 | TYR- 306 | 3.49 | 0 | Hydrophobic |
| C21 | CD2 | TYR- 306 | 3.89 | 0 | Hydrophobic |
| C5 | CZ | TYR- 306 | 4.25 | 0 | Hydrophobic |
| C17 | CB | TYR- 306 | 4.19 | 0 | Hydrophobic |
| O2 | OH | TYR- 306 | 2.54 | 173.28 | H-Bond (Protein Donor) |
| O2 | ZN | ZN- 403 | 2.27 | 0 | Metal Acceptor |
| O4 | ZN | ZN- 403 | 2.13 | 0 | Metal Acceptor |
