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
2010-07-07
| 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: | 36.057 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.694 | 340.875 |
| % Hydrophobic | % Polar |
|---|---|
| 58.42 | 41.58 |
| According to VolSite | |
| HET Code: | EQH |
|---|---|
| Formula: | C18H20N3O2S |
| Molecular weight: | 342.435 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.9 % |
| Polar Surface area: | 120.17 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 25.7252 | 8.50767 | -18.5766 |
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 |
| C09 | CG2 | ILE- 14 | 3.48 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 14 | 4.07 | 0 | Hydrophobic |
| C18 | SG | CYS- 22 | 3.93 | 0 | Hydrophobic |
| O21 | NZ | LYS- 37 | 3.04 | 158.68 | H-Bond (Protein Donor) |
| O21 | NZ | LYS- 37 | 3.04 | 0 | Ionic (Protein Cationic) |
| O22 | NZ | LYS- 37 | 3.46 | 0 | Ionic (Protein Cationic) |
| C24 | CG1 | VAL- 68 | 4.2 | 0 | Hydrophobic |
| O21 | OH | TYR- 70 | 2.83 | 163.91 | H-Bond (Protein Donor) |
| C24 | SD | MET- 86 | 3.68 | 0 | Hydrophobic |
| N01 | O | GLU- 87 | 2.67 | 166.55 | H-Bond (Ligand Donor) |
| C12 | CE1 | TYR- 88 | 3.84 | 0 | Hydrophobic |
| N03 | N | CYS- 89 | 2.99 | 162.31 | H-Bond (Protein Donor) |
| C08 | CB | ASP- 93 | 4.46 | 0 | Hydrophobic |
| S07 | CE2 | PHE- 148 | 3.89 | 0 | Hydrophobic |
| C23 | CE1 | PHE- 148 | 3.36 | 0 | Hydrophobic |
| C24 | CZ | PHE- 148 | 3.87 | 0 | Hydrophobic |
| C19 | CZ | PHE- 148 | 4.44 | 0 | Hydrophobic |
