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
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: | 27.113 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | IOD IOD |
| Ligandability | Volume (Å3) |
|---|---|
| 0.984 | 985.500 |
| % Hydrophobic | % Polar |
|---|---|
| 49.32 | 50.68 |
| According to VolSite | |
| HET Code: | KMP |
|---|---|
| Formula: | C15H8O6 |
| Molecular weight: | 284.220 g/mol |
| DrugBank ID: | DB01852 |
| Buried Surface Area: | 63.2 % |
| Polar Surface area: | 112.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -23.2487 | 1.83314 | -11.6337 |
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 | ALA- 25 | 4.42 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 27 | 3.51 | 0 | Hydrophobic |
| O29 | NZ | LYS- 42 | 3.35 | 141.17 | H-Bond (Protein Donor) |
| O24 | N | VAL- 96 | 2.79 | 149.52 | H-Bond (Protein Donor) |
| C4 | CD1 | ILE- 160 | 3.96 | 0 | Hydrophobic |
| C5 | CB | ASP- 161 | 4.46 | 0 | Hydrophobic |
