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: | 35.161 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.704 | 479.250 |
| % Hydrophobic | % Polar |
|---|---|
| 52.11 | 47.89 |
| According to VolSite | |
| HET Code: | WI2 |
|---|---|
| Formula: | C17H19N4O3 |
| Molecular weight: | 327.358 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.15 % |
| Polar Surface area: | 104.4 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| 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 |
|---|---|---|
| -25.1255 | 8.01483 | 18.2994 |
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 |
| CAG | CG2 | ILE- 14 | 3.75 | 0 | Hydrophobic |
| CAK | SG | CYS- 22 | 3.57 | 0 | Hydrophobic |
| OAD | NZ | LYS- 37 | 3.38 | 123.23 | H-Bond (Protein Donor) |
| OAC | NZ | LYS- 37 | 2.63 | 177.64 | H-Bond (Protein Donor) |
| OAD | NZ | LYS- 37 | 3.38 | 0 | Ionic (Protein Cationic) |
| OAC | NZ | LYS- 37 | 2.63 | 0 | Ionic (Protein Cationic) |
| CAL | CG2 | VAL- 68 | 4.31 | 0 | Hydrophobic |
| CAJ | CG1 | VAL- 68 | 4.26 | 0 | Hydrophobic |
| OAD | OH | TYR- 70 | 3.05 | 158.53 | H-Bond (Protein Donor) |
| CAJ | SD | MET- 86 | 3.68 | 0 | Hydrophobic |
| NAB | O | GLU- 87 | 2.64 | 153.09 | H-Bond (Ligand Donor) |
| NAN | N | CYS- 89 | 2.94 | 167.05 | H-Bond (Protein Donor) |
| CAW | CZ | PHE- 148 | 4.15 | 0 | Hydrophobic |
| CAM | CZ | PHE- 148 | 4.2 | 0 | Hydrophobic |
| CAL | CE1 | PHE- 148 | 3.37 | 0 | Hydrophobic |
| OAD | N | ASP- 159 | 3.23 | 124.41 | H-Bond (Protein Donor) |
| OAD | O | HOH- 2123 | 2.55 | 179.96 | H-Bond (Protein Donor) |
