sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.570 Å
X-ray
2005-06-13
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.890 | 6.140 | 6.000 | 0.270 | 6.520 | 3 |
| 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 |
|---|---|
| A | 93 % |
| D | 7 % |
| B-Factor: | 17.273 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.535 | 428.625 |
| % Hydrophobic | % Polar |
|---|---|
| 70.08 | 29.92 |
| According to VolSite | |
| HET Code: | SHH |
|---|---|
| Formula: | C14H20N2O3 |
| Molecular weight: | 264.320 g/mol |
| DrugBank ID: | DB02546 |
| Buried Surface Area: | 61.35 % |
| 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 |
|---|---|---|
| -6.64574 | -10.4293 | 38.0115 |
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 |
| C6 | CD2 | LEU- 21 | 4 | 0 | Hydrophobic |
| C10 | CB | ASP- 98 | 4.38 | 0 | Hydrophobic |
| C7 | CG2 | ILE- 100 | 3.9 | 0 | Hydrophobic |
| C10 | CG1 | ILE- 100 | 3.67 | 0 | Hydrophobic |
| C7 | CE2 | PHE- 152 | 4.2 | 0 | Hydrophobic |
| C2 | CE1 | PHE- 152 | 3.51 | 0 | Hydrophobic |
| C5 | CZ | PHE- 152 | 3.73 | 0 | Hydrophobic |
| C3 | CD2 | PHE- 208 | 4.06 | 0 | Hydrophobic |
| C4 | CG | PHE- 208 | 3.94 | 0 | Hydrophobic |
| C5 | CE2 | PHE- 208 | 4.01 | 0 | Hydrophobic |
| C6 | CZ | PHE- 208 | 3.81 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 275 | 4.42 | 0 | Hydrophobic |
| C2 | CZ | TYR- 312 | 4.09 | 0 | Hydrophobic |
| C6 | CE1 | PHE- 341 | 3.9 | 0 | Hydrophobic |
| O1 | ZN | ZN- 2451 | 1.9 | 0 | Metal Acceptor |
| O2 | ZN | ZN- 2451 | 2.17 | 0 | Metal Acceptor |
| N2 | O | HOH- 2583 | 2.77 | 162.16 | H-Bond (Ligand Donor) |
