sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2013-02-07
| 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: | 50.297 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.858 | 604.125 |
| % Hydrophobic | % Polar |
|---|---|
| 53.07 | 46.93 |
| According to VolSite | |
| HET Code: | 1J4 |
|---|---|
| Formula: | C27H35F3N7O3 |
| Molecular weight: | 562.607 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 51.2 % |
| Polar Surface area: | 104.13 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 46.9708 | 12.2087 | 34.8011 |
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 |
| N8 | O | LEU- 59 | 3.19 | 154.36 | H-Bond (Ligand Donor) |
| C1 | CD2 | LEU- 59 | 3.94 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 59 | 3.99 | 0 | Hydrophobic |
| C38 | CB | LEU- 59 | 4.2 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 59 | 3.87 | 0 | Hydrophobic |
| C16 | CB | LEU- 59 | 4.07 | 0 | Hydrophobic |
| C37 | SG | CYS- 67 | 4.23 | 0 | Hydrophobic |
| C38 | CB | CYS- 67 | 4.23 | 0 | Hydrophobic |
| F31 | SG | CYS- 67 | 3.43 | 0 | Hydrophobic |
| F31 | CB | ALA- 80 | 4.3 | 0 | Hydrophobic |
| F30 | CD | LYS- 82 | 3.45 | 0 | Hydrophobic |
| F31 | CD1 | LEU- 130 | 3.84 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 132 | 4.05 | 0 | Hydrophobic |
| N22 | N | CYS- 133 | 2.93 | 153.99 | H-Bond (Protein Donor) |
| C1 | CB | ARG- 134 | 4.5 | 0 | Hydrophobic |
| C5 | CG | ARG- 136 | 4.05 | 0 | Hydrophobic |
| C34 | CE2 | PHE- 183 | 3.68 | 0 | Hydrophobic |
