sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.440 Å
X-ray
2011-06-24
| 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 |
|---|---|
| D | 100 % |
| B-Factor: | 41.825 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.291 | 826.875 |
| % Hydrophobic | % Polar |
|---|---|
| 62.04 | 37.96 |
| According to VolSite | |
| HET Code: | JN8 |
|---|---|
| Formula: | C22H27N3O4S2 |
| Molecular weight: | 461.597 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.28 % |
| Polar Surface area: | 144.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 25.8515 | -0.415226 | -9.09542 |
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- 159 | 4.02 | 0 | Hydrophobic |
| C32 | CE | MET- 273 | 4.44 | 0 | Hydrophobic |
| S4 | CD2 | LEU- 319 | 4.47 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 319 | 4.34 | 0 | Hydrophobic |
| C12 | CB | ASN- 321 | 4.29 | 0 | Hydrophobic |
| S17 | CB | ASN- 321 | 3.92 | 0 | Hydrophobic |
| S17 | CB | TRP- 332 | 4.3 | 0 | Hydrophobic |
| S4 | CD1 | ILE- 336 | 4.49 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 336 | 4.34 | 0 | Hydrophobic |
| S17 | CG2 | ILE- 336 | 4.01 | 0 | Hydrophobic |
| C28 | SD | MET- 337 | 3.89 | 0 | Hydrophobic |
| C9 | CE2 | PHE- 340 | 3.95 | 0 | Hydrophobic |
| C27 | CE2 | PHE- 340 | 4.23 | 0 | Hydrophobic |
| C9 | SD | MET- 357 | 3.75 | 0 | Hydrophobic |
| C28 | CB | MET- 357 | 4 | 0 | Hydrophobic |
| C29 | CG | MET- 357 | 3.62 | 0 | Hydrophobic |
| C29 | CB | SER- 368 | 3.59 | 0 | Hydrophobic |
| O31 | NE2 | GLN- 369 | 3.27 | 151.22 | H-Bond (Protein Donor) |
| C32 | CE1 | PHE- 372 | 4.3 | 0 | Hydrophobic |
| C31 | CB | PHE- 372 | 3.64 | 0 | Hydrophobic |
| C32 | CG1 | ILE- 376 | 3.79 | 0 | Hydrophobic |
