sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.240 Å
X-ray
2014-05-02
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.540 | 6.320 | 6.320 | 0.330 | 6.760 | 10 |
| 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 | 19 % |
| B | 81 % |
| B-Factor: | 26.748 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.312 | 2338.875 |
| % Hydrophobic | % Polar |
|---|---|
| 49.35 | 50.65 |
| According to VolSite | |
| HET Code: | SHH |
|---|---|
| Formula: | C14H20N2O3 |
| Molecular weight: | 264.320 g/mol |
| DrugBank ID: | DB02546 |
| Buried Surface Area: | 67.37 % |
| Polar Surface area: | 78.42 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 16.7197 | 36.7932 | 27.4175 |
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 |
| C2 | CZ3 | TRP- 141 | 4.49 | 0 | Hydrophobic |
| O1 | NE2 | HIS- 142 | 2.51 | 142.06 | H-Bond (Protein Donor) |
| N1 | NE2 | HIS- 143 | 2.86 | 150.08 | H-Bond (Ligand Donor) |
| C4 | CE2 | PHE- 152 | 3.72 | 0 | Hydrophobic |
| C5 | CZ | PHE- 152 | 3.97 | 0 | Hydrophobic |
| C6 | CE1 | PHE- 152 | 3.91 | 0 | Hydrophobic |
| C2 | CD2 | PHE- 152 | 3.82 | 0 | Hydrophobic |
| C6 | CG | PHE- 208 | 3.84 | 0 | Hydrophobic |
| C7 | CB | PHE- 208 | 3.96 | 0 | Hydrophobic |
| C5 | CD1 | PHE- 208 | 3.72 | 0 | Hydrophobic |
| C7 | CB | PRO- 273 | 3.96 | 0 | Hydrophobic |
| C10 | CB | PRO- 273 | 3.93 | 0 | Hydrophobic |
| C14 | CG | PRO- 273 | 3.97 | 0 | Hydrophobic |
| C11 | CE | MET- 274 | 3.99 | 0 | Hydrophobic |
| O2 | OH | TYR- 306 | 2.55 | 157.69 | H-Bond (Protein Donor) |
| C2 | CZ | TYR- 306 | 4.43 | 0 | Hydrophobic |
| C13 | CB | TYR- 306 | 3.86 | 0 | Hydrophobic |
| O1 | ZN | ZN- 401 | 2.25 | 0 | Metal Acceptor |
| O2 | ZN | ZN- 401 | 2.22 | 0 | Metal Acceptor |
