sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2001-04-16
| 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: | 20.225 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | MN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.306 | 1181.250 |
| % Hydrophobic | % Polar |
|---|---|
| 41.71 | 58.29 |
| According to VolSite | |
| HET Code: | ANP |
|---|---|
| Formula: | C10H13N6O12P3 |
| Molecular weight: | 502.164 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.73 % |
| Polar Surface area: | 322.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 25.1705 | 29.9849 | 11.6072 |
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 |
| C1' | CB | LEU- 19 | 4.5 | 0 | Hydrophobic |
| O2G | N | PHE- 24 | 2.54 | 150.09 | H-Bond (Protein Donor) |
| C1' | CG2 | VAL- 27 | 4.24 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 27 | 3.91 | 0 | Hydrophobic |
| O1B | NZ | LYS- 42 | 3.7 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 42 | 2.75 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 42 | 2.75 | 146.34 | H-Bond (Protein Donor) |
| N6 | O | GLU- 94 | 2.8 | 160.31 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 96 | 3.25 | 152.1 | H-Bond (Protein Donor) |
| C2' | CG | GLU- 100 | 4.29 | 0 | Hydrophobic |
| O2' | OE2 | GLU- 100 | 2.72 | 153.85 | H-Bond (Ligand Donor) |
| O3' | O | GLU- 143 | 3.23 | 160.24 | H-Bond (Ligand Donor) |
| C2' | CE | MET- 146 | 3.55 | 0 | Hydrophobic |
| C2' | CD1 | ILE- 160 | 3.81 | 0 | Hydrophobic |
| O2B | MN | MN- 3510 | 2.4 | 0 | Metal Acceptor |
| O2A | MN | MN- 3510 | 2.17 | 0 | Metal Acceptor |
