sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 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: | 51.832 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.443 | 563.625 |
| % Hydrophobic | % Polar |
|---|---|
| 47.31 | 52.69 |
| According to VolSite | |
| HET Code: | 1J3 |
|---|---|
| Formula: | C28H38FN8O3 |
| Molecular weight: | 553.652 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.91 % |
| Polar Surface area: | 107.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 34.1069 | -34.7298 | -16.3463 |
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 | CD2 | LEU- 59 | 4.41 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 59 | 3.85 | 0 | Hydrophobic |
| C26 | CB | LEU- 59 | 4.03 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 59 | 3.73 | 0 | Hydrophobic |
| C6 | CB | LEU- 59 | 3.93 | 0 | Hydrophobic |
| N33 | O | LEU- 59 | 3.08 | 157.02 | H-Bond (Ligand Donor) |
| C25 | SG | CYS- 67 | 3.76 | 0 | Hydrophobic |
| C26 | CB | CYS- 67 | 3.83 | 0 | Hydrophobic |
| F19 | SG | CYS- 67 | 3.73 | 0 | Hydrophobic |
| F19 | CD | LYS- 82 | 4.09 | 0 | Hydrophobic |
| F19 | CD1 | LEU- 130 | 4.34 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 132 | 4.02 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 132 | 4.31 | 0 | Hydrophobic |
| N11 | N | CYS- 133 | 2.83 | 161.38 | H-Bond (Protein Donor) |
| C1 | CB | ARG- 134 | 4.27 | 0 | Hydrophobic |
| C5 | CD | ARG- 136 | 4 | 0 | Hydrophobic |
| C4 | CG | ARG- 136 | 4.11 | 0 | Hydrophobic |
| C6 | CG | ARG- 136 | 4.2 | 0 | Hydrophobic |
| C20 | CZ | PHE- 183 | 4.26 | 0 | Hydrophobic |
| C22 | CE2 | PHE- 183 | 3.79 | 0 | Hydrophobic |
