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: | 34.258 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.196 | 418.500 |
| % Hydrophobic | % Polar |
|---|---|
| 66.13 | 33.87 |
| According to VolSite | |
| HET Code: | XK3 |
|---|---|
| Formula: | C17H20N3O2S |
| Molecular weight: | 330.425 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.52 % |
| Polar Surface area: | 120.17 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 25.5424 | 8.29565 | -18.5765 |
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 |
| C02 | CG2 | ILE- 14 | 4.14 | 0 | Hydrophobic |
| S06 | CG2 | ILE- 14 | 4.2 | 0 | Hydrophobic |
| C16 | SG | CYS- 22 | 3.65 | 0 | Hydrophobic |
| O19 | NZ | LYS- 37 | 3.82 | 0 | Ionic (Protein Cationic) |
| O20 | NZ | LYS- 37 | 3.38 | 0 | Ionic (Protein Cationic) |
| O20 | NZ | LYS- 37 | 3.38 | 153.94 | H-Bond (Protein Donor) |
| C21 | CG1 | VAL- 68 | 4.17 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 68 | 4.24 | 0 | Hydrophobic |
| O20 | OH | TYR- 70 | 3.09 | 172.69 | H-Bond (Protein Donor) |
| C21 | SD | MET- 86 | 3.29 | 0 | Hydrophobic |
| N12 | O | GLU- 87 | 2.56 | 147.06 | H-Bond (Ligand Donor) |
| C02 | CE1 | TYR- 88 | 3.84 | 0 | Hydrophobic |
| N10 | N | CYS- 89 | 2.89 | 167.25 | H-Bond (Protein Donor) |
| C14 | CE2 | PHE- 148 | 3.95 | 0 | Hydrophobic |
| C15 | CZ | PHE- 148 | 4.11 | 0 | Hydrophobic |
| C17 | CZ | PHE- 148 | 4.17 | 0 | Hydrophobic |
| C21 | CE1 | PHE- 148 | 4.1 | 0 | Hydrophobic |
| C22 | CZ | PHE- 148 | 3.64 | 0 | Hydrophobic |
| C17 | CE1 | PHE- 160 | 3.63 | 0 | Hydrophobic |
