sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 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: | 42.054 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.397 | 965.250 |
| % Hydrophobic | % Polar |
|---|---|
| 59.09 | 40.91 |
| According to VolSite | |
| HET Code: | 4VQ |
|---|---|
| Formula: | C21H20N3O5 |
| Molecular weight: | 394.401 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 54.04 % |
| Polar Surface area: | 119.62 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 25.482 | -8.6349 | 18.6025 |
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 |
| CAC | CG2 | ILE- 14 | 4.29 | 0 | Hydrophobic |
| CAL | CG2 | ILE- 14 | 3.6 | 0 | Hydrophobic |
| CAH | SG | CYS- 22 | 3.34 | 0 | Hydrophobic |
| OAG | NZ | LYS- 37 | 3.52 | 0 | Ionic (Protein Cationic) |
| OAF | NZ | LYS- 37 | 2.8 | 0 | Ionic (Protein Cationic) |
| OAF | NZ | LYS- 37 | 2.8 | 170.12 | H-Bond (Protein Donor) |
| CAD | CG2 | VAL- 68 | 4.35 | 0 | Hydrophobic |
| CAT | SD | MET- 86 | 3.56 | 0 | Hydrophobic |
| CAK | SD | MET- 86 | 3.67 | 0 | Hydrophobic |
| NAE | O | GLU- 87 | 2.82 | 174.22 | H-Bond (Ligand Donor) |
| NAN | N | CYS- 89 | 3.01 | 172.03 | H-Bond (Protein Donor) |
| CAD | CE1 | PHE- 148 | 3.59 | 0 | Hydrophobic |
| CAK | CZ | PHE- 148 | 3.2 | 0 | Hydrophobic |
