sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 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: | 20.076 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.948 | 705.375 |
| % Hydrophobic | % Polar |
|---|---|
| 51.67 | 48.33 |
| According to VolSite | |
| HET Code: | 2AN |
|---|---|
| Formula: | C16H12NO3S |
| Molecular weight: | 298.336 g/mol |
| DrugBank ID: | DB04474 |
| Buried Surface Area: | 69.2 % |
| Polar Surface area: | 77.61 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -22.4695 | 2.0119 | -10.502 |
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 |
| C4 | CB | LEU- 19 | 3.93 | 0 | Hydrophobic |
| C14 | CB | ALA- 25 | 3.77 | 0 | Hydrophobic |
| C3 | CB | VAL- 27 | 4.28 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 27 | 3.8 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 27 | 3.94 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 27 | 3.8 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 27 | 3.31 | 0 | Hydrophobic |
| C7 | CB | ALA- 40 | 3.87 | 0 | Hydrophobic |
| O2 | NZ | LYS- 42 | 2.75 | 149.32 | H-Bond (Protein Donor) |
| O2 | NZ | LYS- 42 | 2.75 | 0 | Ionic (Protein Cationic) |
| C8 | CG1 | ILE- 77 | 4.02 | 0 | Hydrophobic |
| C7 | CB | LEU- 93 | 4.47 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 93 | 3.84 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 96 | 3.47 | 0 | Hydrophobic |
| C4 | CE | MET- 146 | 3.51 | 0 | Hydrophobic |
| C1 | CD1 | ILE- 160 | 3.65 | 0 | Hydrophobic |
| C8 | CG2 | ILE- 160 | 4.1 | 0 | Hydrophobic |
| C1 | CD1 | ILE- 160 | 3.65 | 0 | Hydrophobic |
| O3 | N | ASP- 161 | 3.42 | 161.22 | H-Bond (Protein Donor) |
| O3 | O | HOH- 482 | 2.89 | 149.18 | H-Bond (Protein Donor) |
