sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 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: | 28.139 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.975 | 452.250 |
| % Hydrophobic | % Polar |
|---|---|
| 56.72 | 43.28 |
| According to VolSite | |
| HET Code: | BX1 |
|---|---|
| Formula: | C19H23N4O5 |
| Molecular weight: | 387.410 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.07 % |
| 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: | 6 |
| X | Y | Z |
|---|---|---|
| -25.5113 | 20.7221 | -18.8331 |
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 |
| C04 | CG2 | ILE- 14 | 3.57 | 0 | Hydrophobic |
| C13 | SG | CYS- 22 | 3.59 | 0 | Hydrophobic |
| O17 | NZ | LYS- 37 | 2.8 | 153.95 | H-Bond (Protein Donor) |
| O17 | NZ | LYS- 37 | 2.8 | 0 | Ionic (Protein Cationic) |
| O18 | NZ | LYS- 37 | 2.95 | 0 | Ionic (Protein Cationic) |
| C19 | CG2 | VAL- 68 | 4.22 | 0 | Hydrophobic |
| O18 | OH | TYR- 70 | 3.08 | 152.25 | H-Bond (Protein Donor) |
| C15 | SD | MET- 86 | 3.95 | 0 | Hydrophobic |
| N10 | O | GLU- 87 | 2.79 | 157.31 | H-Bond (Ligand Donor) |
| C25 | CZ | TYR- 88 | 4.33 | 0 | Hydrophobic |
| N08 | N | CYS- 89 | 2.86 | 163.63 | H-Bond (Protein Donor) |
| C01 | CB | ASP- 93 | 4.24 | 0 | Hydrophobic |
| C28 | CB | SER- 96 | 4.2 | 0 | Hydrophobic |
| C01 | CE2 | PHE- 148 | 4.32 | 0 | Hydrophobic |
| C19 | CE1 | PHE- 148 | 3.76 | 0 | Hydrophobic |
| C20 | CZ | PHE- 148 | 3.46 | 0 | Hydrophobic |
| C14 | CZ | PHE- 148 | 4.11 | 0 | Hydrophobic |
| O18 | N | ASP- 159 | 3.4 | 125.88 | H-Bond (Protein Donor) |
