sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.670 Å
X-ray
2004-11-22
| 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: | 15.489 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.157 | 725.625 |
| % Hydrophobic | % Polar |
|---|---|
| 58.14 | 41.86 |
| According to VolSite | |
| HET Code: | 3DE |
|---|---|
| Formula: | C14H16N2O2 |
| Molecular weight: | 244.289 g/mol |
| DrugBank ID: | DB07051 |
| Buried Surface Area: | 63.12 % |
| Polar Surface area: | 44.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 13.6642 | 5.96344 | 12.5399 |
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 | CZ | TYR- 159 | 3.71 | 0 | Hydrophobic |
| C6 | CG | MET- 273 | 3.69 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 319 | 3.61 | 0 | Hydrophobic |
| C17 | CB | ASN- 321 | 3.95 | 0 | Hydrophobic |
| C17 | CE1 | TYR- 329 | 4.12 | 0 | Hydrophobic |
| C17 | CB | TRP- 332 | 3.86 | 0 | Hydrophobic |
| C17 | CB | THR- 333 | 4.36 | 0 | Hydrophobic |
| C9 | CG1 | ILE- 336 | 4.05 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 336 | 3.76 | 0 | Hydrophobic |
| C12 | CE2 | PHE- 340 | 4.1 | 0 | Hydrophobic |
| C12 | SD | MET- 357 | 3.71 | 0 | Hydrophobic |
| O1 | NE2 | GLN- 369 | 2.99 | 174.12 | H-Bond (Protein Donor) |
| C16 | CE2 | PHE- 372 | 4.09 | 0 | Hydrophobic |
| C12 | CD1 | PHE- 372 | 3.68 | 0 | Hydrophobic |
