sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 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: | 26.843 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.486 | 421.875 |
| % Hydrophobic | % Polar |
|---|---|
| 52.00 | 48.00 |
| According to VolSite | |
| HET Code: | 47X |
|---|---|
| Formula: | C15H10O5 |
| Molecular weight: | 270.237 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62 % |
| Polar Surface area: | 86.99 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -23.2399 | 2.29555 | -11.9873 |
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 |
| CAC | CD1 | LEU- 19 | 4.21 | 0 | Hydrophobic |
| CAE | CG1 | VAL- 27 | 3.95 | 0 | Hydrophobic |
| CAL | CG2 | VAL- 27 | 3.65 | 0 | Hydrophobic |
| CAB | CB | ALA- 40 | 3.48 | 0 | Hydrophobic |
| CAA | CD1 | ILE- 77 | 4.02 | 0 | Hydrophobic |
| CAD | CD1 | LEU- 93 | 3.97 | 0 | Hydrophobic |
| OAS | O | GLU- 94 | 2.56 | 167.19 | H-Bond (Ligand Donor) |
| OAS | N | VAL- 96 | 2.8 | 141.86 | H-Bond (Protein Donor) |
| CAC | CE | MET- 146 | 4.22 | 0 | Hydrophobic |
| CAE | CD1 | ILE- 160 | 3.87 | 0 | Hydrophobic |
| CAD | CG2 | ILE- 160 | 4.32 | 0 | Hydrophobic |
| CAK | CD1 | ILE- 160 | 3.99 | 0 | Hydrophobic |
