sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2009-07-20
| 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: | 33.728 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.387 | 675.000 |
| % Hydrophobic | % Polar |
|---|---|
| 55.50 | 44.50 |
| According to VolSite | |
| HET Code: | MRK |
|---|---|
| Formula: | C14H12FN5OS2 |
| Molecular weight: | 349.406 g/mol |
| DrugBank ID: | DB08210 |
| Buried Surface Area: | 68.95 % |
| Polar Surface area: | 139.37 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -9.89048 | 2.80022 | 21.0648 |
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 | CG1 | VAL- 62 | 3.47 | 0 | Hydrophobic |
| N4 | N | ARG- 63 | 3.06 | 158.69 | H-Bond (Protein Donor) |
| N6 | O | ARG- 63 | 3.32 | 170.47 | H-Bond (Ligand Donor) |
| C9 | CG | PRO- 66 | 3.83 | 0 | Hydrophobic |
| C22 | CE | MET- 210 | 3.74 | 0 | Hydrophobic |
| S16 | CD1 | ILE- 211 | 4.11 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 211 | 3.55 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 211 | 3.47 | 0 | Hydrophobic |
| F14 | CD2 | TYR- 214 | 3.28 | 0 | Hydrophobic |
| C21 | CE1 | TYR- 214 | 3.62 | 0 | Hydrophobic |
| C22 | CD1 | TYR- 214 | 4.1 | 0 | Hydrophobic |
| N23 | OH | TYR- 215 | 3.38 | 154.18 | H-Bond (Ligand Donor) |
| C21 | CG | GLU- 221 | 3.74 | 0 | Hydrophobic |
| C22 | CG | GLU- 221 | 4.37 | 0 | Hydrophobic |
| S16 | CE | MET- 235 | 3.88 | 0 | Hydrophobic |
| C21 | CG | MET- 235 | 4.35 | 0 | Hydrophobic |
| C22 | CG | MET- 235 | 3.94 | 0 | Hydrophobic |
| S1 | CG1 | VAL- 452 | 3.97 | 0 | Hydrophobic |
| S1 | CG1 | VAL- 455 | 3.63 | 0 | Hydrophobic |
