sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2008-11-14
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.780 | 6.780 | 6.780 | 0.000 | 6.780 | 1 |
| 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: | 15.564 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.058 | 452.250 |
| % Hydrophobic | % Polar |
|---|---|
| 58.21 | 41.79 |
| According to VolSite | |
| HET Code: | MRK |
|---|---|
| Formula: | C14H12FN5OS2 |
| Molecular weight: | 349.406 g/mol |
| DrugBank ID: | DB08210 |
| Buried Surface Area: | 74.6 % |
| 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 |
|---|---|---|
| -9.52622 | 2.77687 | 20.6458 |
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 | 2.87 | 167.9 | H-Bond (Protein Donor) |
| N6 | O | ARG- 63 | 2.91 | 168.95 | H-Bond (Ligand Donor) |
| C10 | CG | PRO- 66 | 4.18 | 0 | Hydrophobic |
| S16 | CE | MET- 210 | 4.32 | 0 | Hydrophobic |
| C22 | CE | MET- 210 | 3.88 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 211 | 4.35 | 0 | Hydrophobic |
| F14 | CD1 | ILE- 211 | 3.54 | 0 | Hydrophobic |
| S16 | CD1 | ILE- 211 | 3.66 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 211 | 3.5 | 0 | Hydrophobic |
| F14 | CD2 | TYR- 214 | 3.4 | 0 | Hydrophobic |
| C22 | CD1 | TYR- 214 | 3.93 | 0 | Hydrophobic |
| N23 | OH | TYR- 215 | 3.1 | 156.41 | H-Bond (Ligand Donor) |
| C22 | CG | GLU- 221 | 4.07 | 0 | Hydrophobic |
| S16 | CE | MET- 235 | 3.67 | 0 | Hydrophobic |
| C22 | CG | MET- 235 | 3.89 | 0 | Hydrophobic |
| S1 | CG1 | VAL- 452 | 3.83 | 0 | Hydrophobic |
| S1 | CG1 | VAL- 455 | 3.65 | 0 | Hydrophobic |
| S1 | CB | ALA- 456 | 4.45 | 0 | Hydrophobic |
