sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2005-05-03
| Name: | cAMP-specific 3',5'-cyclic phosphodiesterase 4D |
|---|---|
| ID: | PDE4D_HUMAN |
| AC: | Q08499 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.1.4.53 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 27.188 |
|---|---|
| Number of residues: | 19 |
| Including | |
| Standard Amino Acids: | 18 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.968 | 742.500 |
| % Hydrophobic | % Polar |
|---|---|
| 54.09 | 45.91 |
| According to VolSite | |
| HET Code: | IBM |
|---|---|
| Formula: | C10H14N4O2 |
| Molecular weight: | 222.244 g/mol |
| DrugBank ID: | DB07954 |
| Buried Surface Area: | 40.62 % |
| Polar Surface area: | 69.3 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 21.4886 | -5.89281 | 30.2829 |
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 |
| C10 | CE2 | PHE- 340 | 4.4 | 0 | Hydrophobic |
| C14 | CZ | PHE- 340 | 3.23 | 0 | Hydrophobic |
| C10 | SD | MET- 357 | 3.36 | 0 | Hydrophobic |
| C13 | CE | MET- 357 | 4 | 0 | Hydrophobic |
| O6 | NE2 | GLN- 369 | 2.93 | 159.35 | H-Bond (Protein Donor) |
| C10 | CB | PHE- 372 | 3.99 | 0 | Hydrophobic |
