sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.050 Å
X-ray
2009-10-06
| 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: | 31.635 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.141 | 762.750 |
| % Hydrophobic | % Polar |
|---|---|
| 58.41 | 41.59 |
| According to VolSite | |
| HET Code: | 0MO |
|---|---|
| Formula: | C15H22N2O3 |
| Molecular weight: | 278.347 g/mol |
| DrugBank ID: | DB06842 |
| Buried Surface Area: | 62.59 % |
| Polar Surface area: | 59.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 24.1875 | -8.05685 | 15.4792 |
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 |
| C11 | CD2 | LEU- 319 | 4.16 | 0 | Hydrophobic |
| C7 | CB | ASN- 321 | 4.09 | 0 | Hydrophobic |
| C7 | CE1 | TYR- 329 | 3.93 | 0 | Hydrophobic |
| C7 | CB | TRP- 332 | 4.27 | 0 | Hydrophobic |
| C7 | CB | THR- 333 | 4.3 | 0 | Hydrophobic |
| C7 | CG2 | ILE- 336 | 4.09 | 0 | Hydrophobic |
| C8 | CB | ILE- 336 | 4.39 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 336 | 3.82 | 0 | Hydrophobic |
| C15 | CG1 | ILE- 336 | 4.28 | 0 | Hydrophobic |
| C1 | CG2 | ILE- 336 | 4.25 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 336 | 3.71 | 0 | Hydrophobic |
| C1 | SD | MET- 337 | 3.58 | 0 | Hydrophobic |
| C1 | CE2 | PHE- 340 | 3.35 | 0 | Hydrophobic |
| C13 | CZ | PHE- 340 | 3.74 | 0 | Hydrophobic |
| C1 | CB | MET- 357 | 4.22 | 0 | Hydrophobic |
| C3 | SD | MET- 357 | 3.84 | 0 | Hydrophobic |
| C2 | CB | SER- 368 | 4.02 | 0 | Hydrophobic |
| O1 | NE2 | GLN- 369 | 3.2 | 145.34 | H-Bond (Protein Donor) |
| O2 | NE2 | GLN- 369 | 3.07 | 139.64 | H-Bond (Protein Donor) |
| C3 | CB | PHE- 372 | 4.26 | 0 | Hydrophobic |
| C4 | CG | PHE- 372 | 3.81 | 0 | Hydrophobic |
| C7 | CE2 | PHE- 372 | 4.45 | 0 | Hydrophobic |
| C11 | CZ | PHE- 372 | 4.12 | 0 | Hydrophobic |
| C5 | CE2 | PHE- 372 | 3.38 | 0 | Hydrophobic |
