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
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: | 11.222 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.131 | 799.875 |
| % Hydrophobic | % Polar |
|---|---|
| 55.27 | 44.73 |
| According to VolSite | |
| HET Code: | 5DE |
|---|---|
| Formula: | C14H17N3O2 |
| Molecular weight: | 259.304 g/mol |
| DrugBank ID: | DB03183 |
| Buried Surface Area: | 62.96 % |
| Polar Surface area: | 70.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 13.6657 | 5.73016 | 12.689 |
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 |
| C6 | CZ | TYR- 159 | 3.83 | 0 | Hydrophobic |
| C12 | CG | MET- 273 | 3.6 | 0 | Hydrophobic |
| N14 | OD2 | ASP- 318 | 3.31 | 127.27 | H-Bond (Ligand Donor) |
| C11 | CD2 | LEU- 319 | 3.54 | 0 | Hydrophobic |
| C18 | CB | ASN- 321 | 3.76 | 0 | Hydrophobic |
| C18 | CE1 | TYR- 329 | 4 | 0 | Hydrophobic |
| C18 | CB | TRP- 332 | 3.82 | 0 | Hydrophobic |
| C18 | CB | THR- 333 | 4.41 | 0 | Hydrophobic |
| C6 | CG1 | ILE- 336 | 4.2 | 0 | Hydrophobic |
| C17 | CG2 | ILE- 336 | 3.73 | 0 | Hydrophobic |
| C9 | CE2 | PHE- 340 | 4.15 | 0 | Hydrophobic |
| C9 | SD | MET- 357 | 3.82 | 0 | Hydrophobic |
| O19 | NE2 | GLN- 369 | 2.95 | 174.27 | H-Bond (Protein Donor) |
| C17 | CE2 | PHE- 372 | 4.15 | 0 | Hydrophobic |
| C9 | CD1 | PHE- 372 | 3.81 | 0 | Hydrophobic |
| C6 | CZ | PHE- 372 | 4.42 | 0 | Hydrophobic |
