sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 Å
X-ray
2007-10-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.520 | 9.300 | 9.660 | 0.550 | 9.720 | 3 |
| 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: | 38.846 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.480 | 580.500 |
| % Hydrophobic | % Polar |
|---|---|
| 45.93 | 54.07 |
| According to VolSite | |
| HET Code: | R78 |
|---|---|
| Formula: | C28H40N7O3 |
| Molecular weight: | 522.662 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 53.39 % |
| 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: | 7 |
| X | Y | Z |
|---|---|---|
| -47.0029 | 12.2036 | 16.6726 |
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 |
| C7 | CD1 | LEU- 59 | 4.02 | 0 | Hydrophobic |
| C31 | CD2 | LEU- 59 | 4.41 | 0 | Hydrophobic |
| C15 | CB | LEU- 59 | 3.89 | 0 | Hydrophobic |
| C19 | CB | LEU- 59 | 3.97 | 0 | Hydrophobic |
| C17 | CD2 | LEU- 59 | 3.69 | 0 | Hydrophobic |
| N6 | O | LEU- 59 | 3.05 | 157.23 | H-Bond (Ligand Donor) |
| C9 | SG | CYS- 67 | 3.79 | 0 | Hydrophobic |
| C15 | CB | CYS- 67 | 3.7 | 0 | Hydrophobic |
| C10 | CB | ALA- 80 | 3.87 | 0 | Hydrophobic |
| C10 | CB | LYS- 82 | 4.41 | 0 | Hydrophobic |
| C9 | CD | LYS- 82 | 4.29 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 130 | 4.22 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 132 | 4.44 | 0 | Hydrophobic |
| C31 | CD1 | LEU- 132 | 4.07 | 0 | Hydrophobic |
| N1 | N | CYS- 133 | 2.89 | 158.72 | H-Bond (Protein Donor) |
| N5 | O | CYS- 133 | 3.06 | 127.15 | H-Bond (Ligand Donor) |
| C31 | CB | ARG- 134 | 4.26 | 0 | Hydrophobic |
| C18 | CD | ARG- 136 | 3.71 | 0 | Hydrophobic |
| C17 | CG | ARG- 136 | 3.84 | 0 | Hydrophobic |
| C5 | CZ | PHE- 183 | 3.45 | 0 | Hydrophobic |
| C8 | CE2 | PHE- 183 | 3.97 | 0 | Hydrophobic |
