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
2009-02-04
| 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 |
|---|---|
| C | 100 % |
| B-Factor: | 26.617 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.269 | 918.000 |
| % Hydrophobic | % Polar |
|---|---|
| 54.41 | 45.59 |
| According to VolSite | |
| HET Code: | 988 |
|---|---|
| Formula: | C21H15N3O2 |
| Molecular weight: | 341.363 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.57 % |
| Polar Surface area: | 71.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -18.3838 | 7.62177 | 36.3302 |
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 |
| C37 | SD | MET- 439 | 4.29 | 0 | Hydrophobic |
| C43 | CG | MET- 439 | 3.78 | 0 | Hydrophobic |
| C35 | CD2 | LEU- 485 | 4.05 | 0 | Hydrophobic |
| C6 | CB | ASN- 487 | 4.13 | 0 | Hydrophobic |
| C6 | CB | TRP- 498 | 4.37 | 0 | Hydrophobic |
| C13 | CG1 | ILE- 502 | 4.38 | 0 | Hydrophobic |
| C19 | CG1 | ILE- 502 | 4.43 | 0 | Hydrophobic |
| C28 | CG2 | ILE- 502 | 4.21 | 0 | Hydrophobic |
| C39 | CD1 | ILE- 502 | 4.45 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 502 | 3.92 | 0 | Hydrophobic |
| C27 | SD | MET- 503 | 3.94 | 0 | Hydrophobic |
| C26 | CG | MET- 523 | 3.42 | 0 | Hydrophobic |
| C26 | CB | SER- 534 | 3.85 | 0 | Hydrophobic |
| N4 | NE2 | GLN- 535 | 2.82 | 145.73 | H-Bond (Protein Donor) |
| C35 | CZ | PHE- 538 | 4.48 | 0 | Hydrophobic |
| C24 | CG | PHE- 538 | 3.44 | 0 | Hydrophobic |
