sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.470 Å
X-ray
2012-08-10
| Name: | Lactoylglutathione lyase |
|---|---|
| ID: | LGUL_HUMAN |
| AC: | Q04760 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 4.4.1.5 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 48 % |
| B | 52 % |
| B-Factor: | 19.071 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.226 | 671.625 |
| % Hydrophobic | % Polar |
|---|---|
| 70.85 | 29.15 |
| According to VolSite | |
| HET Code: | HPJ |
|---|---|
| Formula: | C22H20N3O3 |
| Molecular weight: | 374.412 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.25 % |
| Polar Surface area: | 70.42 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 9.74068 | -12.5874 | -28.3906 |
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 |
| O21 | NE2 | GLN- 33 | 2.94 | 149.73 | H-Bond (Protein Donor) |
| C28 | SG | CYS- 60 | 3.57 | 0 | Hydrophobic |
| C5 | CE | MET- 65 | 4.06 | 0 | Hydrophobic |
| C9 | CE | MET- 65 | 3.84 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 69 | 4.45 | 0 | Hydrophobic |
| C23 | CD1 | LEU- 69 | 3.7 | 0 | Hydrophobic |
| C28 | CG2 | ILE- 88 | 3.99 | 0 | Hydrophobic |
| C22 | CD1 | LEU- 92 | 4.25 | 0 | Hydrophobic |
| C28 | CD2 | LEU- 92 | 4.48 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 149 | 3.99 | 0 | Hydrophobic |
| C1 | CB | LYS- 150 | 3.89 | 0 | Hydrophobic |
| C16 | SD | MET- 157 | 4.44 | 0 | Hydrophobic |
| C25 | SD | MET- 157 | 4.17 | 0 | Hydrophobic |
| C10 | CE | MET- 157 | 3.49 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 160 | 4.25 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 160 | 3.78 | 0 | Hydrophobic |
| C3 | CE1 | PHE- 162 | 3.69 | 0 | Hydrophobic |
| C3 | CZ3 | TRP- 170 | 3.79 | 0 | Hydrophobic |
| C27 | CB | MET- 179 | 4.02 | 0 | Hydrophobic |
| C24 | CE | MET- 179 | 3.48 | 0 | Hydrophobic |
| C25 | CD1 | LEU- 182 | 4.18 | 0 | Hydrophobic |
| C26 | CB | LEU- 182 | 3.9 | 0 | Hydrophobic |
| C27 | SD | MET- 183 | 3.6 | 0 | Hydrophobic |
| O18 | ZN | ZN- 201 | 2.31 | 0 | Metal Acceptor |
| O21 | ZN | ZN- 201 | 2.22 | 0 | Metal Acceptor |
