sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.400 Å
X-ray
2015-06-10
| Name: | Death-associated protein kinase 1 |
|---|---|
| ID: | DAPK1_HUMAN |
| AC: | P53355 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 18.895 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | BR BR |
| Ligandability | Volume (Å3) |
|---|---|
| 0.888 | 486.000 |
| % Hydrophobic | % Polar |
|---|---|
| 55.56 | 44.44 |
| According to VolSite | |
| HET Code: | GEN |
|---|---|
| Formula: | C15H9O5 |
| Molecular weight: | 269.229 g/mol |
| DrugBank ID: | DB01645 |
| Buried Surface Area: | 67.77 % |
| Polar Surface area: | 89.82 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -22.7099 | 2.10605 | -10.912 |
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 |
| C15 | CD1 | LEU- 19 | 4.14 | 0 | Hydrophobic |
| C16 | CB | LEU- 19 | 4.44 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 27 | 4.31 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 27 | 3.77 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 27 | 4.06 | 0 | Hydrophobic |
| C14 | CB | ALA- 40 | 3.62 | 0 | Hydrophobic |
| C4 | CD | LYS- 42 | 4.14 | 0 | Hydrophobic |
| O4 | NZ | LYS- 42 | 2.84 | 139.13 | H-Bond (Protein Donor) |
| C13 | CD1 | ILE- 77 | 4.07 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 93 | 4.03 | 0 | Hydrophobic |
| O14 | O | GLU- 94 | 2.67 | 174.17 | H-Bond (Ligand Donor) |
| C14 | CB | VAL- 96 | 4.47 | 0 | Hydrophobic |
| O14 | N | VAL- 96 | 2.77 | 139.05 | H-Bond (Protein Donor) |
| C15 | CE | MET- 146 | 3.99 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 160 | 4.18 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 160 | 3.89 | 0 | Hydrophobic |
| C12 | CG2 | ILE- 160 | 4.34 | 0 | Hydrophobic |
| C4 | CB | ASP- 161 | 4.13 | 0 | Hydrophobic |
