sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 Å
X-ray
2014-05-06
| Name: | Phosphodiesterase |
|---|---|
| ID: | Q8WQX9_9TRYP |
| AC: | Q8WQX9 |
| Organism: | Trypanosoma brucei |
| Reign: | Eukaryota |
| TaxID: | 5691 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 26.002 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | ZN MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.087 | 901.125 |
| % Hydrophobic | % Polar |
|---|---|
| 48.31 | 51.69 |
| According to VolSite | |
| HET Code: | PIL |
|---|---|
| Formula: | C18H18Cl2N2O3 |
| Molecular weight: | 381.253 g/mol |
| DrugBank ID: | DB01791 |
| Buried Surface Area: | 55.39 % |
| Polar Surface area: | 60.45 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 8.33104 | 71.4492 | 68.2381 |
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 |
| C19 | CG | MET- 785 | 3.81 | 0 | Hydrophobic |
| CL20 | SD | MET- 785 | 4.04 | 0 | Hydrophobic |
| CL20 | CB | ASP- 822 | 4.13 | 0 | Hydrophobic |
| CL20 | CB | ILE- 823 | 4.21 | 0 | Hydrophobic |
| C12 | CB | ASN- 825 | 4.18 | 0 | Hydrophobic |
| C11 | CB | ASN- 825 | 3.56 | 0 | Hydrophobic |
| C11 | CB | TRP- 836 | 3.92 | 0 | Hydrophobic |
| C11 | CB | ALA- 837 | 4.03 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 840 | 3.65 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 840 | 3.78 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 840 | 4.02 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 840 | 3.68 | 0 | Hydrophobic |
| CL25 | CZ | PHE- 844 | 3.42 | 0 | Hydrophobic |
| C5 | CE2 | PHE- 844 | 4.4 | 0 | Hydrophobic |
| O10 | NE2 | GLN- 874 | 3.47 | 157.55 | H-Bond (Protein Donor) |
| O3 | NE2 | GLN- 874 | 3.36 | 133.43 | H-Bond (Protein Donor) |
| N16 | O | HOH- 1273 | 2.8 | 136.44 | H-Bond (Ligand Donor) |
