sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2015-08-04
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.700 | 7.090 | 7.160 | 0.260 | 7.350 | 5 |
| 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 | 22 % |
| B | 78 % |
| B-Factor: | 26.471 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.058 | 2727.000 |
| % Hydrophobic | % Polar |
|---|---|
| 53.59 | 46.41 |
| According to VolSite | |
| HET Code: | TSN |
|---|---|
| Formula: | C17H22N2O3 |
| Molecular weight: | 302.368 g/mol |
| DrugBank ID: | DB04297 |
| Buried Surface Area: | 65.37 % |
| Polar Surface area: | 69.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 2.54759 | 2.46259 | -28.6462 |
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 |
| C16 | CG | LYS- 33 | 4.48 | 0 | Hydrophobic |
| C16 | CZ | TYR- 100 | 4.15 | 0 | Hydrophobic |
| O1 | NE2 | HIS- 142 | 3.01 | 129.36 | H-Bond (Protein Donor) |
| N1 | NE2 | HIS- 143 | 3 | 127.55 | H-Bond (Ligand Donor) |
| C8 | CZ | PHE- 152 | 4.33 | 0 | Hydrophobic |
| C15 | CE1 | PHE- 152 | 3.52 | 0 | Hydrophobic |
| C17 | CE1 | PHE- 152 | 3.9 | 0 | Hydrophobic |
| C14 | CB | PHE- 208 | 3.68 | 0 | Hydrophobic |
| C15 | CE1 | PHE- 208 | 4.04 | 0 | Hydrophobic |
| C14 | CB | PRO- 273 | 4.02 | 0 | Hydrophobic |
| C1 | CB | PRO- 273 | 3.77 | 0 | Hydrophobic |
| C2 | CE | MET- 274 | 4.47 | 0 | Hydrophobic |
| C3 | CE | MET- 274 | 3.56 | 0 | Hydrophobic |
| O2 | OH | TYR- 306 | 2.55 | 170.49 | H-Bond (Protein Donor) |
| C4 | CB | TYR- 306 | 4.48 | 0 | Hydrophobic |
| C17 | CD2 | TYR- 306 | 3.54 | 0 | Hydrophobic |
| C16 | CD2 | TYR- 306 | 3.73 | 0 | Hydrophobic |
| O1 | ZN | ZN- 401 | 2.64 | 0 | Metal Acceptor |
| O2 | ZN | ZN- 401 | 2.25 | 0 | Metal Acceptor |
