sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2006-11-30
| 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: | 33.966 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.859 | 479.250 |
| % Hydrophobic | % Polar |
|---|---|
| 54.93 | 45.07 |
| According to VolSite | |
| HET Code: | 5Z5 |
|---|---|
| Formula: | C17H16ClN3O2 |
| Molecular weight: | 329.781 g/mol |
| DrugBank ID: | DB07180 |
| Buried Surface Area: | 54.65 % |
| Polar Surface area: | 73.99 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -3.59935 | 9.65817 | 18.8671 |
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 | CG2 | ILE- 14 | 4.25 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 14 | 4.43 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 35 | 3.99 | 0 | Hydrophobic |
| DuAr | NZ | LYS- 37 | 3.96 | 33.79 | Pi/Cation |
| C3 | CG1 | VAL- 68 | 3.52 | 0 | Hydrophobic |
| C2 | CG | MET- 86 | 4.08 | 0 | Hydrophobic |
| C3 | CB | MET- 86 | 3.62 | 0 | Hydrophobic |
| N1 | O | GLU- 87 | 2.76 | 156.48 | H-Bond (Ligand Donor) |
| C15 | CE1 | TYR- 88 | 3.81 | 0 | Hydrophobic |
| O1 | N | CYS- 89 | 2.85 | 165.1 | H-Bond (Protein Donor) |
| C14 | CE2 | PHE- 148 | 4.25 | 0 | Hydrophobic |
| CL1 | CZ | PHE- 148 | 3.89 | 0 | Hydrophobic |
| C4 | CZ | PHE- 148 | 3.42 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 162 | 4.25 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 162 | 4.33 | 0 | Hydrophobic |
| CL1 | CD1 | LEU- 166 | 4.34 | 0 | Hydrophobic |
