sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.380 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: | 32.027 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.515 | 1910.250 |
| % Hydrophobic | % Polar |
|---|---|
| 46.11 | 53.89 |
| According to VolSite | |
| HET Code: | SHH |
|---|---|
| Formula: | C14H20N2O3 |
| Molecular weight: | 264.320 g/mol |
| DrugBank ID: | DB02546 |
| Buried Surface Area: | 61.17 % |
| 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 |
|---|---|---|
| 0.962895 | -38.7448 | 28.3237 |
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 |
| O1 | NE2 | HIS- 142 | 2.64 | 155 | H-Bond (Protein Donor) |
| N1 | NE2 | HIS- 143 | 2.88 | 141.35 | H-Bond (Ligand Donor) |
| C2 | CD1 | PHE- 152 | 3.7 | 0 | Hydrophobic |
| C5 | CZ | PHE- 152 | 3.46 | 0 | Hydrophobic |
| C4 | CE1 | PHE- 152 | 3.59 | 0 | Hydrophobic |
| C3 | CD1 | PHE- 208 | 4.34 | 0 | Hydrophobic |
| C4 | CE1 | PHE- 208 | 4.26 | 0 | Hydrophobic |
| C6 | CG | PHE- 208 | 3.58 | 0 | Hydrophobic |
| C7 | CB | PHE- 208 | 4 | 0 | Hydrophobic |
| C7 | CB | PRO- 273 | 3.83 | 0 | Hydrophobic |
| C10 | CB | PRO- 273 | 4.24 | 0 | Hydrophobic |
| C14 | CG | PRO- 273 | 4.07 | 0 | Hydrophobic |
| C11 | CE | MET- 274 | 4.16 | 0 | Hydrophobic |
| O2 | OH | TYR- 306 | 2.64 | 171.18 | H-Bond (Protein Donor) |
| C2 | CZ | TYR- 306 | 4.31 | 0 | Hydrophobic |
| C13 | CB | TYR- 306 | 3.89 | 0 | Hydrophobic |
| O1 | ZN | ZN- 403 | 2.08 | 0 | Metal Acceptor |
| O2 | ZN | ZN- 403 | 2.17 | 0 | Metal Acceptor |
