sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.210 Å
X-ray
2013-07-24
| Name: | Histone deacetylase |
|---|---|
| ID: | A5H660_SCHMA |
| AC: | A5H660 |
| Organism: | Schistosoma mansoni |
| Reign: | Eukaryota |
| TaxID: | 6183 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 86 % |
| D | 14 % |
| B-Factor: | 19.519 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.695 | 550.125 |
| % Hydrophobic | % Polar |
|---|---|
| 49.08 | 50.92 |
| According to VolSite | |
| HET Code: | J38 |
|---|---|
| Formula: | C10H10N2O3S |
| Molecular weight: | 238.263 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.91 % |
| Polar Surface area: | 103.72 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 55.5097 | 11.1819 | 39.8321 |
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 |
| O11 | NE2 | HIS- 141 | 2.82 | 169.2 | H-Bond (Protein Donor) |
| N10 | NE2 | HIS- 142 | 2.73 | 139.2 | H-Bond (Ligand Donor) |
| C01 | CZ | PHE- 151 | 3.78 | 0 | Hydrophobic |
| C05 | CB | PHE- 216 | 4.05 | 0 | Hydrophobic |
| N14 | NE2 | HIS- 292 | 3.12 | 156.66 | H-Bond (Ligand Donor) |
| O09 | ZN | ZN- 500 | 2.72 | 0 | Metal Acceptor |
| O11 | ZN | ZN- 500 | 2.31 | 0 | Metal Acceptor |
