sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.450 Å
X-ray
2012-11-11
| Name: | 3-ketoacyl-CoA thiolase-like protein |
|---|---|
| ID: | E9AW84_LEIMU |
| AC: | E9AW84 |
| Organism: | Leishmania mexicana |
| Reign: | Eukaryota |
| TaxID: | 929439 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 100 % |
| B-Factor: | 18.491 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.340 | 894.375 |
| % Hydrophobic | % Polar |
|---|---|
| 58.49 | 41.51 |
| According to VolSite | |
| HET Code: | COA |
|---|---|
| Formula: | C21H32N7O16P3S |
| Molecular weight: | 763.502 g/mol |
| DrugBank ID: | DB01992 |
| Buried Surface Area: | 36.17 % |
| Polar Surface area: | 426.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 21 |
| H-Bond Donors: | 6 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 18 |
| X | Y | Z |
|---|---|---|
| -43.5617 | 54.901 | -31.2997 |
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 |
| S1P | CB | ALA- 123 | 3.35 | 0 | Hydrophobic |
| O9A | NE | ARG- 159 | 3.46 | 152.03 | H-Bond (Protein Donor) |
| C6P | CD1 | LEU- 165 | 3.8 | 0 | Hydrophobic |
| C5B | CZ | PHE- 180 | 4.23 | 0 | Hydrophobic |
| C6P | CG | PRO- 183 | 3.99 | 0 | Hydrophobic |
| C1B | CG2 | VAL- 241 | 3.88 | 0 | Hydrophobic |
| C4B | CB | PHE- 243 | 4.26 | 0 | Hydrophobic |
| CEP | CZ | PHE- 243 | 4.03 | 0 | Hydrophobic |
| C1B | CB | PHE- 243 | 3.73 | 0 | Hydrophobic |
| CEP | CG | MET- 255 | 4.28 | 0 | Hydrophobic |
| S1P | CB | CYS- 340 | 3.94 | 0 | Hydrophobic |
| C6P | CZ | PHE- 341 | 4.38 | 0 | Hydrophobic |
| S1P | O | HOH- 2020 | 2.54 | 179.96 | Weak HBond PROT |
