sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.330 Å
X-ray
2011-12-23
| Name: | Phosphodiesterase |
|---|---|
| ID: | Q53I60_TRYCR |
| AC: | Q53I60 |
| Organism: | Trypanosoma cruzi |
| Reign: | Eukaryota |
| TaxID: | 5693 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| G | 87 % |
| H | 13 % |
| B-Factor: | 22.911 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.771 | 1788.750 |
| % Hydrophobic | % Polar |
|---|---|
| 58.87 | 41.13 |
| According to VolSite | |
| HET Code: | WYQ |
|---|---|
| Formula: | C21H26N5O6S |
| Molecular weight: | 476.526 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 47.59 % |
| Polar Surface area: | 151.42 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -41.41 | 25.472 | -47.9235 |
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 |
| C12 | CZ | TYR- 367 | 3.89 | 0 | Hydrophobic |
| C9 | CG | MET- 482 | 4.07 | 0 | Hydrophobic |
| C13 | CB | ILE- 522 | 4.19 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 538 | 4.37 | 0 | Hydrophobic |
| C11 | CG1 | ILE- 538 | 4.27 | 0 | Hydrophobic |
| C12 | CG1 | ILE- 538 | 3.85 | 0 | Hydrophobic |
| C6 | CZ | PHE- 542 | 3.49 | 0 | Hydrophobic |
| C21 | CE2 | PHE- 560 | 3.28 | 0 | Hydrophobic |
| O1 | NE2 | GLN- 570 | 3.16 | 155.55 | H-Bond (Protein Donor) |
| C16 | CE1 | PHE- 573 | 4.34 | 0 | Hydrophobic |
| C18 | CB | PHE- 573 | 3.64 | 0 | Hydrophobic |
| C13 | CZ | PHE- 573 | 4.24 | 0 | Hydrophobic |
| C16 | CZ | PHE- 577 | 3.5 | 0 | Hydrophobic |
