sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.930 Å
X-ray
2014-11-12
| Name: | Leukotriene A-4 hydrolase |
|---|---|
| ID: | LKHA4_HUMAN |
| AC: | P09960 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.3.2.6 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 17.467 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.326 | 2116.125 |
| % Hydrophobic | % Polar |
|---|---|
| 39.39 | 60.61 |
| According to VolSite | |
| HET Code: | B3N |
|---|---|
| Formula: | C16H25N3O3 |
| Molecular weight: | 307.388 g/mol |
| DrugBank ID: | DB02565 |
| Buried Surface Area: | 78.85 % |
| Polar Surface area: | 81.67 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -29.8974 | -1.89959 | 0.685273 |
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 |
| C9 | CG | GLN- 136 | 4.27 | 0 | Hydrophobic |
| C8 | CB | GLN- 136 | 4.41 | 0 | Hydrophobic |
| C14 | CB | ALA- 137 | 4.06 | 0 | Hydrophobic |
| C9 | CZ | TYR- 267 | 4.22 | 0 | Hydrophobic |
| C8 | CE2 | TYR- 267 | 3.76 | 0 | Hydrophobic |
| C7 | CG | TYR- 267 | 4.03 | 0 | Hydrophobic |
| C6 | CD1 | TYR- 267 | 3.75 | 0 | Hydrophobic |
| C5 | CB | TYR- 267 | 4.37 | 0 | Hydrophobic |
| N3 | O | GLY- 269 | 2.95 | 167.22 | H-Bond (Ligand Donor) |
| C7 | SD | MET- 270 | 4.04 | 0 | Hydrophobic |
| C18 | CB | TRP- 311 | 4.18 | 0 | Hydrophobic |
| C21 | CB | PHE- 314 | 3.77 | 0 | Hydrophobic |
| C9 | CZ | PHE- 314 | 4.43 | 0 | Hydrophobic |
| C18 | CB | PHE- 314 | 3.68 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 314 | 3.99 | 0 | Aromatic Face/Face |
| C22 | CD1 | PHE- 362 | 4.46 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 367 | 3.61 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 369 | 4.38 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 369 | 3.92 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 369 | 3.96 | 0 | Hydrophobic |
| C16 | CB | PRO- 374 | 3.82 | 0 | Hydrophobic |
| C22 | CB | ALA- 377 | 3.5 | 0 | Hydrophobic |
| C9 | CE1 | TYR- 378 | 4.16 | 0 | Hydrophobic |
| C6 | CZ | TYR- 378 | 3.93 | 0 | Hydrophobic |
| C15 | CB | TYR- 378 | 3.92 | 0 | Hydrophobic |
| O2 | OH | TYR- 383 | 2.59 | 159.96 | H-Bond (Protein Donor) |
| O2 | ZN | ZN- 702 | 1.95 | 0 | Metal Acceptor |
| O4 | ZN | ZN- 702 | 2.04 | 0 | Metal Acceptor |
