sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.980 Å
X-ray
2010-08-05
| 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: | 25.600 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.802 | 448.875 |
| % Hydrophobic | % Polar |
|---|---|
| 55.64 | 44.36 |
| According to VolSite | |
| HET Code: | WCX |
|---|---|
| Formula: | C29H30F3N4O3 |
| Molecular weight: | 539.569 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.15 % |
| Polar Surface area: | 83.81 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -26.375 | -2.4239 | 18.8647 |
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 |
| C11 | CD1 | ILE- 14 | 4.22 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 14 | 4 | 0 | Hydrophobic |
| F38 | CG1 | ILE- 14 | 3.65 | 0 | Hydrophobic |
| C01 | CZ | TYR- 19 | 3.77 | 0 | Hydrophobic |
| F37 | CZ | TYR- 19 | 4.14 | 0 | Hydrophobic |
| C02 | SG | CYS- 22 | 4.33 | 0 | Hydrophobic |
| C05 | SG | CYS- 22 | 4.25 | 0 | Hydrophobic |
| F37 | CB | CYS- 22 | 3.26 | 0 | Hydrophobic |
| C25 | CG1 | VAL- 68 | 3.88 | 0 | Hydrophobic |
| C25 | SD | MET- 86 | 3.82 | 0 | Hydrophobic |
| C14 | CE1 | TYR- 88 | 4.26 | 0 | Hydrophobic |
| N09 | N | CYS- 89 | 2.72 | 169.29 | H-Bond (Protein Donor) |
| C33 | CB | ASP- 93 | 4.03 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 148 | 3.8 | 0 | Aromatic Face/Face |
| N28 | OD1 | ASP- 159 | 2.87 | 141.72 | H-Bond (Ligand Donor) |
| O29 | N | ASP- 159 | 2.8 | 165.95 | H-Bond (Protein Donor) |
| C01 | CZ | PHE- 160 | 4.06 | 0 | Hydrophobic |
