sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.170 Å
X-ray
2009-08-24
| Name: | Serine/threonine-protein kinase Nek2 |
|---|---|
| ID: | NEK2_HUMAN |
| AC: | P51955 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.169 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.912 | 452.250 |
| % Hydrophobic | % Polar |
|---|---|
| 56.72 | 43.28 |
| According to VolSite | |
| HET Code: | VGK |
|---|---|
| Formula: | C21H19N2O5 |
| Molecular weight: | 379.386 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.48 % |
| Polar Surface area: | 106.73 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 25.4847 | -9.25804 | 18.7888 |
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 |
| C25 | CG2 | ILE- 14 | 4.47 | 0 | Hydrophobic |
| C28 | CG2 | ILE- 14 | 4.36 | 0 | Hydrophobic |
| C06 | CD1 | ILE- 14 | 3.97 | 0 | Hydrophobic |
| C22 | CG2 | ILE- 14 | 3.5 | 0 | Hydrophobic |
| C14 | SG | CYS- 22 | 3.74 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 35 | 4.49 | 0 | Hydrophobic |
| O18 | NZ | LYS- 37 | 2.96 | 149.1 | H-Bond (Protein Donor) |
| O18 | NZ | LYS- 37 | 2.96 | 0 | Ionic (Protein Cationic) |
| C19 | CG1 | VAL- 68 | 4.23 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 68 | 4.23 | 0 | Hydrophobic |
| O17 | OH | TYR- 70 | 2.91 | 173.54 | H-Bond (Protein Donor) |
| C19 | SD | MET- 86 | 3.56 | 0 | Hydrophobic |
| N10 | O | GLU- 87 | 2.73 | 159.69 | H-Bond (Ligand Donor) |
| N08 | N | CYS- 89 | 2.95 | 169.78 | H-Bond (Protein Donor) |
| C25 | CB | ASP- 93 | 4.49 | 0 | Hydrophobic |
| C20 | CE1 | PHE- 148 | 3.45 | 0 | Hydrophobic |
| O17 | N | ASP- 159 | 2.67 | 131.19 | H-Bond (Protein Donor) |
