sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2009-07-14
| 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: | 59.281 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.127 | 705.375 |
| % Hydrophobic | % Polar |
|---|---|
| 59.81 | 40.19 |
| According to VolSite | |
| HET Code: | EV1 |
|---|---|
| Formula: | C20H21NO4 |
| Molecular weight: | 339.385 g/mol |
| DrugBank ID: | DB01113 |
| Buried Surface Area: | 55.17 % |
| Polar Surface area: | 49.81 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 0 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 22.5787 | -8.5434 | 16.9455 |
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 |
| C15 | CE | MET- 273 | 4.18 | 0 | Hydrophobic |
| C23 | CE | MET- 273 | 3.86 | 0 | Hydrophobic |
| C13 | CG | MET- 273 | 3.53 | 0 | Hydrophobic |
| C23 | CB | HIS- 276 | 4.04 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 319 | 4.35 | 0 | Hydrophobic |
| C19 | CB | ASN- 321 | 4.13 | 0 | Hydrophobic |
| C19 | CE1 | TYR- 329 | 4.38 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 336 | 3.97 | 0 | Hydrophobic |
| C1 | CG1 | ILE- 336 | 4.15 | 0 | Hydrophobic |
| C19 | CG2 | ILE- 336 | 3.77 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 336 | 4.15 | 0 | Hydrophobic |
| C4 | CG1 | ILE- 336 | 4.02 | 0 | Hydrophobic |
| C11 | CZ | PHE- 340 | 3.63 | 0 | Hydrophobic |
| C21 | CE | MET- 357 | 3.38 | 0 | Hydrophobic |
| O20 | NE2 | GLN- 369 | 3.27 | 140.35 | H-Bond (Protein Donor) |
| C21 | CG | PHE- 372 | 3.44 | 0 | Hydrophobic |
| C19 | CE2 | PHE- 372 | 4.48 | 0 | Hydrophobic |
| C6 | CE2 | PHE- 372 | 3.35 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 376 | 4.15 | 0 | Hydrophobic |
