sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.350 Å
X-ray
2012-11-02
| 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 | 53 % |
| B | 44 % |
| D | 3 % |
| B-Factor: | 20.017 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.295 | 766.125 |
| % Hydrophobic | % Polar |
|---|---|
| 46.26 | 53.74 |
| According to VolSite | |
| HET Code: | HPU |
|---|---|
| Formula: | C18H15N2O4S |
| Molecular weight: | 355.388 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.77 % |
| Polar Surface area: | 97.92 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 20.668 | -8.9772 | 18.5009 |
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 |
| O19 | NE2 | GLN- 33 | 2.85 | 148.36 | H-Bond (Protein Donor) |
| C24 | SG | CYS- 60 | 3.67 | 0 | Hydrophobic |
| C1 | CE1 | PHE- 67 | 3.49 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 69 | 4.4 | 0 | Hydrophobic |
| C20 | CD1 | LEU- 69 | 3.64 | 0 | Hydrophobic |
| C24 | CG2 | ILE- 88 | 4.17 | 0 | Hydrophobic |
| C20 | CD1 | LEU- 92 | 4.41 | 0 | Hydrophobic |
| C1 | CG2 | THR- 101 | 3.79 | 0 | Hydrophobic |
| C14 | CE | MET- 157 | 4.16 | 0 | Hydrophobic |
| C27 | SD | MET- 157 | 3.93 | 0 | Hydrophobic |
| C11 | CE | MET- 157 | 3.31 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 160 | 4.13 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 160 | 3.95 | 0 | Hydrophobic |
| C25 | CB | MET- 179 | 3.97 | 0 | Hydrophobic |
| C22 | CE | MET- 179 | 3.53 | 0 | Hydrophobic |
| C26 | CB | LEU- 182 | 4.05 | 0 | Hydrophobic |
| C27 | CD1 | LEU- 182 | 4.49 | 0 | Hydrophobic |
| C25 | SD | MET- 183 | 3.55 | 0 | Hydrophobic |
| O16 | ZN | ZN- 201 | 2.11 | 0 | Metal Acceptor |
| O19 | ZN | ZN- 201 | 2.11 | 0 | Metal Acceptor |
| O4 | O | HOH- 1065 | 2.62 | 147.38 | H-Bond (Protein Donor) |
