sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2011-06-13
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 22.851 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.124 | 553.500 |
| % Hydrophobic | % Polar |
|---|---|
| 65.85 | 34.15 |
| According to VolSite | |
| HET Code: | 1DI |
|---|---|
| Formula: | C17H17Cl2N2O |
| Molecular weight: | 336.236 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.3 % |
| Polar Surface area: | 47.95 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 8.65032 | 14.3544 | -23.0425 |
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 |
| CL8 | CD1 | ILE- 34 | 3.35 | 0 | Hydrophobic |
| CL8 | CH2 | TRP- 141 | 3.74 | 0 | Hydrophobic |
| CL11 | CD2 | TRP- 141 | 4.16 | 0 | Hydrophobic |
| N1 | NE2 | HIS- 142 | 2.88 | 178.91 | H-Bond (Ligand Donor) |
| C5 | CB | PHE- 152 | 4.31 | 0 | Hydrophobic |
| CL11 | SG | CYS- 153 | 4.11 | 0 | Hydrophobic |
| C3 | SG | CYS- 153 | 3.9 | 0 | Hydrophobic |
| C17 | CG | PHE- 208 | 3.38 | 0 | Hydrophobic |
