sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2003-04-23
| 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: | 19.949 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.460 | 432.000 |
| % Hydrophobic | % Polar |
|---|---|
| 45.31 | 54.69 |
| According to VolSite | |
| HET Code: | DRG |
|---|---|
| Formula: | C12H11N3 |
| Molecular weight: | 197.236 g/mol |
| DrugBank ID: | DB04069 |
| Buried Surface Area: | 69.48 % |
| Polar Surface area: | 51.8 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 23.9496 | 28.4972 | 10.9953 |
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 | CB | LEU- 19 | 4.2 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 19 | 4.2 | 0 | Hydrophobic |
| N3 | O | SER- 21 | 3.49 | 145.23 | H-Bond (Ligand Donor) |
| C14 | CG2 | VAL- 27 | 3.78 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 27 | 4.07 | 0 | Hydrophobic |
| C8 | CB | ALA- 40 | 3.52 | 0 | Hydrophobic |
| N2 | NZ | LYS- 42 | 3.17 | 145.71 | H-Bond (Protein Donor) |
| C9 | CD1 | ILE- 77 | 3.87 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 93 | 3.79 | 0 | Hydrophobic |
| C8 | CB | VAL- 96 | 3.87 | 0 | Hydrophobic |
| C6 | CE | MET- 146 | 3.75 | 0 | Hydrophobic |
| C10 | CG2 | ILE- 160 | 4.5 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 160 | 3.43 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 160 | 3.91 | 0 | Hydrophobic |
