sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.960 Å
X-ray
2010-08-31
| Name: | Leukotriene A-4 hydrolase homolog |
|---|---|
| ID: | LKHA4_YEAST |
| AC: | Q10740 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | 3.3.2.6 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 31.199 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.798 | 1329.750 |
| % Hydrophobic | % Polar |
|---|---|
| 35.28 | 64.72 |
| According to VolSite | |
| HET Code: | BES |
|---|---|
| Formula: | C16H24N2O4 |
| Molecular weight: | 308.373 g/mol |
| DrugBank ID: | DB03424 |
| Buried Surface Area: | 59.57 % |
| Polar Surface area: | 117.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -24.2938 | -1.53964 | 13.7573 |
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 |
| N2 | OE1 | GLU- 186 | 2.84 | 149.38 | H-Bond (Ligand Donor) |
| N2 | OE1 | GLU- 186 | 2.84 | 0 | Ionic (Ligand Cationic) |
| C11 | CB | GLU- 186 | 4.06 | 0 | Hydrophobic |
| C10 | CG | GLU- 186 | 3.73 | 0 | Hydrophobic |
| C6 | CD1 | TYR- 312 | 4.26 | 0 | Hydrophobic |
| C12 | CE1 | TYR- 312 | 3.4 | 0 | Hydrophobic |
| O4 | N | GLY- 313 | 2.63 | 155.71 | H-Bond (Protein Donor) |
| O4 | N | GLY- 314 | 3.42 | 153.71 | H-Bond (Protein Donor) |
| N2 | OE1 | GLU- 316 | 2.76 | 166.29 | H-Bond (Ligand Donor) |
| N2 | OE1 | GLU- 316 | 2.76 | 0 | Ionic (Ligand Cationic) |
| N2 | OE2 | GLU- 316 | 3.81 | 0 | Ionic (Ligand Cationic) |
| C15 | CB | HIS- 340 | 3.83 | 0 | Hydrophobic |
| O2 | OE2 | GLU- 341 | 3.17 | 163.24 | H-Bond (Ligand Donor) |
| O3 | OH | TYR- 429 | 2.97 | 153.4 | H-Bond (Protein Donor) |
| C16 | CE2 | TYR- 429 | 3.66 | 0 | Hydrophobic |
| O2 | ZN | ZN- 1672 | 2.36 | 0 | Metal Acceptor |
| O3 | ZN | ZN- 1672 | 2.39 | 0 | Metal Acceptor |
| O1 | O | HOH- 2342 | 2.74 | 154.44 | H-Bond (Protein Donor) |
