sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2013-01-24
| 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: | 36.154 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.263 | 651.375 |
| % Hydrophobic | % Polar |
|---|---|
| 66.84 | 33.16 |
| According to VolSite | |
| HET Code: | 1J9 |
|---|---|
| Formula: | C21H18Cl2N6O4 |
| Molecular weight: | 489.311 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.13 % |
| Polar Surface area: | 124.28 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 53.7739 | 23.3399 | -18.0208 |
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 |
| C13 | CG1 | VAL- 62 | 3.66 | 0 | Hydrophobic |
| N5 | O | ARG- 63 | 2.71 | 174.54 | H-Bond (Ligand Donor) |
| N6 | N | ARG- 63 | 2.94 | 172.7 | H-Bond (Protein Donor) |
| C12 | CG2 | THR- 65 | 4.11 | 0 | Hydrophobic |
| C6 | CB | GLU- 67 | 4.42 | 0 | Hydrophobic |
| N4 | N | GLY- 68 | 3.12 | 149.94 | H-Bond (Protein Donor) |
| CL2 | CB | SER- 69 | 3.9 | 0 | Hydrophobic |
| C3 | CB | SER- 69 | 4.06 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 91 | 4.24 | 0 | Hydrophobic |
| C2 | CB | TRP- 99 | 4.07 | 0 | Hydrophobic |
| CL1 | CG1 | ILE- 159 | 3.62 | 0 | Hydrophobic |
| C20 | CG1 | ILE- 159 | 4.21 | 0 | Hydrophobic |
| C14 | CE | MET- 210 | 3.77 | 0 | Hydrophobic |
| C15 | CD2 | TYR- 214 | 3.38 | 0 | Hydrophobic |
| C14 | SD | MET- 235 | 3.71 | 0 | Hydrophobic |
| CL2 | CB | LEU- 451 | 3.51 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 451 | 4.29 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 452 | 3.55 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 455 | 4.21 | 0 | Hydrophobic |
| CL2 | CG2 | VAL- 455 | 3.68 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 455 | 3.37 | 0 | Hydrophobic |
| C19 | CB | ALA- 456 | 4.27 | 0 | Hydrophobic |
| CL1 | CB | ALA- 456 | 4.06 | 0 | Hydrophobic |
| DuAr | NZ | LYS- 459 | 3.72 | 152.24 | Pi/Cation |
| O3 | O | HOH- 737 | 2.68 | 179.95 | H-Bond (Protein Donor) |
