sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2010-08-05
| 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: | 30.565 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.704 | 411.750 |
| % Hydrophobic | % Polar |
|---|---|
| 59.02 | 40.98 |
| According to VolSite | |
| HET Code: | WGZ |
|---|---|
| Formula: | C27H28F3N4O3S |
| Molecular weight: | 545.596 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.33 % |
| Polar Surface area: | 112.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 26.1504 | 10.7141 | -18.3447 |
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 | CD1 | ILE- 14 | 4.31 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 14 | 3.41 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 14 | 3.82 | 0 | Hydrophobic |
| F38 | CG2 | ILE- 14 | 3.3 | 0 | Hydrophobic |
| F38 | CB | CYS- 22 | 3.39 | 0 | Hydrophobic |
| DuAr | NZ | LYS- 37 | 3.17 | 142.44 | Pi/Cation |
| S24 | CG1 | VAL- 68 | 4.22 | 0 | Hydrophobic |
| N09 | N | CYS- 89 | 2.67 | 165.97 | H-Bond (Protein Donor) |
| C32 | CB | ASP- 93 | 4.1 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 148 | 3.94 | 0 | Aromatic Face/Face |
| N27 | O | ASP- 159 | 2.77 | 169.06 | H-Bond (Ligand Donor) |
| O28 | N | ASP- 159 | 3.01 | 158.76 | H-Bond (Protein Donor) |
| C01 | CB | ALA- 163 | 4.09 | 0 | Hydrophobic |
| C01 | CD2 | LEU- 166 | 3.57 | 0 | Hydrophobic |
| F36 | CD2 | LEU- 166 | 3.88 | 0 | Hydrophobic |
