sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2012-01-09
| Name: | Glucokinase |
|---|---|
| ID: | HXK4_HUMAN |
| AC: | P35557 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.1.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.999 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.298 | 708.750 |
| % Hydrophobic | % Polar |
|---|---|
| 55.24 | 44.76 |
| According to VolSite | |
| HET Code: | 0H4 |
|---|---|
| Formula: | C20H22F3N3O2 |
| Molecular weight: | 393.403 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.41 % |
| Polar Surface area: | 62.3 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -8.83832 | 3.04186 | 19.7432 |
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 |
| C10 | CG1 | VAL- 62 | 3.78 | 0 | Hydrophobic |
| N2 | O | ARG- 63 | 2.87 | 173.94 | H-Bond (Ligand Donor) |
| C16 | CB | ARG- 63 | 3.96 | 0 | Hydrophobic |
| C1 | CG | PRO- 66 | 4.19 | 0 | Hydrophobic |
| C16 | CB | PRO- 66 | 3.57 | 0 | Hydrophobic |
| C20 | CG1 | ILE- 159 | 3.83 | 0 | Hydrophobic |
| C15 | CE | MET- 210 | 3.54 | 0 | Hydrophobic |
| C10 | CG1 | ILE- 211 | 4.2 | 0 | Hydrophobic |
| C15 | CG1 | ILE- 211 | 4.03 | 0 | Hydrophobic |
| C11 | CD2 | TYR- 214 | 4.29 | 0 | Hydrophobic |
| C14 | CD1 | TYR- 214 | 3.7 | 0 | Hydrophobic |
| C15 | CG | TYR- 214 | 4.34 | 0 | Hydrophobic |
| F2 | CD2 | TYR- 214 | 3.6 | 0 | Hydrophobic |
| C13 | CE1 | TYR- 214 | 3.95 | 0 | Hydrophobic |
| F3 | CE2 | TYR- 214 | 3.98 | 0 | Hydrophobic |
| F1 | CD1 | TYR- 215 | 4.28 | 0 | Hydrophobic |
| F2 | CD1 | TYR- 215 | 3.75 | 0 | Hydrophobic |
| C14 | SD | MET- 235 | 3.87 | 0 | Hydrophobic |
| F1 | CD2 | LEU- 451 | 3.52 | 0 | Hydrophobic |
| F2 | CD1 | LEU- 451 | 4.19 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 455 | 3.74 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 455 | 4.23 | 0 | Hydrophobic |
| C20 | CB | ALA- 456 | 4.34 | 0 | Hydrophobic |
