sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2010-08-31
| Name: | Serine/threonine-protein kinase VRK1 |
|---|---|
| ID: | VRK1_HUMAN |
| AC: | Q99986 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 44.543 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.556 | 621.000 |
| % Hydrophobic | % Polar |
|---|---|
| 42.39 | 57.61 |
| According to VolSite | |
| HET Code: | REB |
|---|---|
| Formula: | C18H17N7 |
| Molecular weight: | 331.374 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 55.82 % |
| Polar Surface area: | 102.31 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 25.2411 | -8.95148 | 61.9022 |
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 | CD1 | ILE- 43 | 3.71 | 0 | Hydrophobic |
| C24 | CA | PHE- 48 | 4.47 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 51 | 4.06 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 51 | 3.56 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 51 | 3.61 | 0 | Hydrophobic |
| C02 | CB | PRO- 111 | 4.21 | 0 | Hydrophobic |
| C02 | CB | MET- 131 | 3.84 | 0 | Hydrophobic |
| N08 | O | ASP- 132 | 2.98 | 146.81 | H-Bond (Ligand Donor) |
| N13 | N | PHE- 134 | 2.85 | 167.42 | H-Bond (Protein Donor) |
| C02 | CE2 | PHE- 134 | 3.46 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 184 | 4.23 | 0 | Hydrophobic |
| C02 | CG1 | VAL- 196 | 4.3 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 196 | 4.15 | 0 | Hydrophobic |
| N04 | O | HOH- 369 | 2.74 | 158 | H-Bond (Protein Donor) |
