sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2006-03-26
| Name: | Histone deacetylase-like amidohydrolase |
|---|---|
| ID: | HDAH_ALCSD |
| AC: | Q70I53 |
| Organism: | Alcaligenes sp. ) |
| Reign: | Bacteria |
| TaxID: | 242601 |
| EC Number: | 3.5.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 85 % |
| D | 15 % |
| B-Factor: | 24.690 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.408 | 526.500 |
| % Hydrophobic | % Polar |
|---|---|
| 66.03 | 33.97 |
| According to VolSite | |
| HET Code: | CF3 |
|---|---|
| Formula: | C15H18F3NO2 |
| Molecular weight: | 301.304 g/mol |
| DrugBank ID: | DB07553 |
| Buried Surface Area: | 65.66 % |
| Polar Surface area: | 46.17 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -2.63705 | 36.509 | 18.1926 |
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 |
| C5 | CD1 | LEU- 21 | 3.6 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 21 | 3.76 | 0 | Hydrophobic |
| C1 | CB | ALA- 22 | 4.14 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 100 | 4.48 | 0 | Hydrophobic |
| C4 | CG2 | ILE- 100 | 3.96 | 0 | Hydrophobic |
| F2 | CB | PRO- 140 | 3.79 | 0 | Hydrophobic |
| F1 | CG | PRO- 140 | 3.39 | 0 | Hydrophobic |
| C8 | CZ | PHE- 152 | 4.38 | 0 | Hydrophobic |
| C9 | CE1 | PHE- 152 | 4.1 | 0 | Hydrophobic |
| C11 | CD1 | PHE- 152 | 3.95 | 0 | Hydrophobic |
| F1 | CD1 | PHE- 152 | 3.99 | 0 | Hydrophobic |
| C7 | CE1 | PHE- 152 | 3.66 | 0 | Hydrophobic |
| C15 | SG | CYS- 153 | 4.34 | 0 | Hydrophobic |
| C10 | CD1 | PHE- 208 | 3.54 | 0 | Hydrophobic |
| C8 | CE1 | PHE- 208 | 3.68 | 0 | Hydrophobic |
| C6 | CG | PHE- 208 | 3.71 | 0 | Hydrophobic |
| C7 | CD2 | PHE- 208 | 3.96 | 0 | Hydrophobic |
| F2 | CB | GLU- 309 | 3.85 | 0 | Hydrophobic |
| O2 | OH | TYR- 312 | 2.73 | 176.16 | H-Bond (Protein Donor) |
| F1 | CZ | TYR- 312 | 4.3 | 0 | Hydrophobic |
| C4 | CB | PHE- 341 | 4.27 | 0 | Hydrophobic |
| C10 | CD1 | PHE- 341 | 3.73 | 0 | Hydrophobic |
| C8 | CE1 | PHE- 341 | 4.47 | 0 | Hydrophobic |
| C5 | CB | PHE- 341 | 3.56 | 0 | Hydrophobic |
