sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.240 Å
X-ray
2007-11-29
| Name: | Death-associated protein kinase 3 |
|---|---|
| ID: | DAPK3_HUMAN |
| AC: | O43293 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 18.550 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 0.820 | 438.750 |
| % Hydrophobic | % Polar |
|---|---|
| 56.15 | 43.85 |
| According to VolSite | |
| HET Code: | 7CP |
|---|---|
| Formula: | C18H19Cl2N4O |
| Molecular weight: | 378.276 g/mol |
| DrugBank ID: | DB07242 |
| Buried Surface Area: | 56.31 % |
| Polar Surface area: | 62.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 14.3971 | 21.373 | 29.3485 |
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 |
| C1B | CB | LEU- 19 | 4.2 | 0 | Hydrophobic |
| CL1F | CD1 | LEU- 19 | 4.35 | 0 | Hydrophobic |
| C1V | CG2 | VAL- 27 | 4.1 | 0 | Hydrophobic |
| C1U | CG1 | VAL- 27 | 4.12 | 0 | Hydrophobic |
| C1T | CG2 | VAL- 27 | 3.82 | 0 | Hydrophobic |
| CL1F | CB | ALA- 40 | 4.46 | 0 | Hydrophobic |
| CL1E | CB | ALA- 40 | 3.72 | 0 | Hydrophobic |
| CL1E | CD1 | ILE- 77 | 3.9 | 0 | Hydrophobic |
| CL1E | CB | LEU- 93 | 4.14 | 0 | Hydrophobic |
| C1H | CD1 | LEU- 93 | 3.84 | 0 | Hydrophobic |
| C1B | CE | MET- 146 | 4.03 | 0 | Hydrophobic |
| CL1F | CE | MET- 146 | 3.52 | 0 | Hydrophobic |
| C1L | CD1 | ILE- 160 | 3.57 | 0 | Hydrophobic |
| C1P | CG2 | ILE- 160 | 4.48 | 0 | Hydrophobic |
| C1V | CD1 | ILE- 160 | 4.26 | 0 | Hydrophobic |
| C1T | CD1 | ILE- 160 | 3.63 | 0 | Hydrophobic |
| C1I | CD1 | ILE- 160 | 3.64 | 0 | Hydrophobic |
| N1W | OD2 | ASP- 161 | 3.96 | 0 | Ionic (Ligand Cationic) |
