sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.990 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: | 37.071 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.040 | 553.500 |
| % Hydrophobic | % Polar |
|---|---|
| 59.76 | 40.24 |
| According to VolSite | |
| HET Code: | 30E |
|---|---|
| Formula: | C21H27N4O5 |
| Molecular weight: | 415.463 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.1 % |
| Polar Surface area: | 122.86 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -25.8088 | 20.6112 | -18.6008 |
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 | CG2 | ILE- 14 | 3.81 | 0 | Hydrophobic |
| C04 | SG | CYS- 22 | 4.39 | 0 | Hydrophobic |
| C01 | SG | CYS- 22 | 3.48 | 0 | Hydrophobic |
| C01 | CG2 | VAL- 35 | 4.24 | 0 | Hydrophobic |
| O29 | NZ | LYS- 37 | 3.81 | 0 | Ionic (Protein Cationic) |
| C01 | CB | LYS- 37 | 3.92 | 0 | Hydrophobic |
| C25 | CG1 | VAL- 68 | 4.22 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 68 | 4.2 | 0 | Hydrophobic |
| C01 | CE | MET- 86 | 3.77 | 0 | Hydrophobic |
| C25 | SD | MET- 86 | 3.33 | 0 | Hydrophobic |
| N24 | O | GLU- 87 | 2.67 | 160.77 | H-Bond (Ligand Donor) |
| C19 | CE1 | TYR- 88 | 4.14 | 0 | Hydrophobic |
| N22 | N | CYS- 89 | 2.78 | 161.98 | H-Bond (Protein Donor) |
| C16 | CB | SER- 96 | 4.12 | 0 | Hydrophobic |
| C26 | CE2 | PHE- 148 | 3.72 | 0 | Hydrophobic |
| C04 | CZ | PHE- 148 | 3.79 | 0 | Hydrophobic |
