sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.790 Å
X-ray
2012-01-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.300 | 6.300 | 6.300 | 0.000 | 6.300 | 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: | 26.001 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.373 | 735.750 |
| % Hydrophobic | % Polar |
|---|---|
| 61.93 | 38.07 |
| According to VolSite | |
| HET Code: | 4DC |
|---|---|
| Formula: | C18H22N2O3S2 |
| Molecular weight: | 378.509 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.66 % |
| Polar Surface area: | 112.74 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 5.06156 | -8.73112 | -2.73512 |
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 |
| C15 | CG1 | VAL- 62 | 4.36 | 0 | Hydrophobic |
| N7 | O | ARG- 63 | 2.91 | 161.26 | H-Bond (Ligand Donor) |
| N21 | N | ARG- 63 | 2.97 | 176.39 | H-Bond (Protein Donor) |
| C3 | CG | PRO- 66 | 3.65 | 0 | Hydrophobic |
| S18 | CB | GLU- 67 | 4.16 | 0 | Hydrophobic |
| C23 | CG | GLN- 98 | 3.47 | 0 | Hydrophobic |
| C14 | CE | MET- 210 | 3.74 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 211 | 4.05 | 0 | Hydrophobic |
| C12 | CE1 | TYR- 214 | 3.97 | 0 | Hydrophobic |
| C13 | CD1 | TYR- 214 | 3.68 | 0 | Hydrophobic |
| C14 | CG | TYR- 214 | 3.9 | 0 | Hydrophobic |
| C16 | CZ | TYR- 214 | 4.27 | 0 | Hydrophobic |
| C15 | SD | MET- 235 | 4.41 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 451 | 4.49 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 451 | 4.48 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 455 | 3.74 | 0 | Hydrophobic |
| S18 | CG1 | VAL- 455 | 4.28 | 0 | Hydrophobic |
| S18 | CB | LYS- 458 | 3.84 | 0 | Hydrophobic |
