sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2009-01-08
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.360 | 6.360 | 6.360 | 0.000 | 6.360 | 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: | 41.568 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.286 | 600.750 |
| % Hydrophobic | % Polar |
|---|---|
| 60.11 | 39.89 |
| According to VolSite | |
| HET Code: | AJB |
|---|---|
| Formula: | C14H14N6OS2 |
| Molecular weight: | 346.431 g/mol |
| DrugBank ID: | DB07358 |
| Buried Surface Area: | 67.12 % |
| Polar Surface area: | 152.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| 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 |
|---|---|---|
| 39.886 | 16.1654 | 61.8501 |
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 |
| C5 | CG1 | VAL- 62 | 3.61 | 0 | Hydrophobic |
| C1 | CD | ARG- 63 | 3.66 | 0 | Hydrophobic |
| N17 | N | ARG- 63 | 3.02 | 163.96 | H-Bond (Protein Donor) |
| N19 | O | ARG- 63 | 3.05 | 130.77 | H-Bond (Ligand Donor) |
| C4 | CG | PRO- 66 | 4.02 | 0 | Hydrophobic |
| C10 | CB | PRO- 66 | 3.83 | 0 | Hydrophobic |
| C2 | CE | MET- 210 | 4.07 | 0 | Hydrophobic |
| S23 | CE | MET- 210 | 4.29 | 0 | Hydrophobic |
| S23 | CD1 | ILE- 211 | 4.48 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 211 | 3.87 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 211 | 3.75 | 0 | Hydrophobic |
| C2 | CD1 | TYR- 214 | 3.77 | 0 | Hydrophobic |
| N15 | OH | TYR- 215 | 2.86 | 146.07 | H-Bond (Ligand Donor) |
| C2 | CG | GLU- 221 | 4.17 | 0 | Hydrophobic |
| C2 | CG | MET- 235 | 3.62 | 0 | Hydrophobic |
| S23 | CE | MET- 235 | 3.56 | 0 | Hydrophobic |
| S22 | CG1 | VAL- 452 | 3.84 | 0 | Hydrophobic |
| S22 | CG1 | VAL- 455 | 3.47 | 0 | Hydrophobic |
