sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2008-05-17
| Name: | Serine/threonine-protein kinase PLK |
|---|---|
| ID: | Q4KMI8_DANRE |
| AC: | Q4KMI8 |
| Organism: | Danio rerio |
| Reign: | Eukaryota |
| TaxID: | 7955 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 58.592 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.019 | 955.125 |
| % Hydrophobic | % Polar |
|---|---|
| 45.58 | 54.42 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.01 % |
| Polar Surface area: | 260.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 46.0077 | 19.9763 | 76.7354 |
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 | CYS- 53 | 3.98 | 0 | Hydrophobic |
| O1B | NZ | LYS- 68 | 3.03 | 133.33 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 68 | 3.03 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 68 | 3.7 | 0 | Ionic (Protein Cationic) |
| N6 | O | GLU- 117 | 2.99 | 159.64 | H-Bond (Ligand Donor) |
| N1 | N | CYS- 119 | 3.01 | 149.66 | H-Bond (Protein Donor) |
| C2' | CE1 | PHE- 169 | 4.07 | 0 | Hydrophobic |
