sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2007-02-15
| Name: | Serine/threonine-protein kinase PLK1 |
|---|---|
| ID: | PLK1_HUMAN |
| AC: | P53350 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.21 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 20.238 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.597 | 621.000 |
| % Hydrophobic | % Polar |
|---|---|
| 44.02 | 55.98 |
| According to VolSite | |
| HET Code: | 626 |
|---|---|
| Formula: | C23H25N6O2S |
| Molecular weight: | 449.549 g/mol |
| DrugBank ID: | DB07186 |
| Buried Surface Area: | 59.03 % |
| Polar Surface area: | 115.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -0.140125 | 24.3759 | 67.6237 |
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 |
| C14 | CB | LEU- 59 | 3.74 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 59 | 3.87 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 59 | 3.98 | 0 | Hydrophobic |
| S29 | CB | CYS- 67 | 4.37 | 0 | Hydrophobic |
| N4 | O | GLU- 131 | 2.89 | 155.38 | H-Bond (Ligand Donor) |
| N6 | N | CYS- 133 | 2.94 | 156.03 | H-Bond (Protein Donor) |
| N7 | O | CYS- 133 | 3.15 | 137.37 | H-Bond (Ligand Donor) |
| C20 | CD | ARG- 136 | 4.2 | 0 | Hydrophobic |
| C12 | CG | ARG- 136 | 3.73 | 0 | Hydrophobic |
| C26 | CG | ARG- 136 | 3.59 | 0 | Hydrophobic |
| C32 | CZ | PHE- 183 | 3.76 | 0 | Hydrophobic |
