sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.720 Å
X-ray
2004-10-06
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 10.418 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.182 | 833.625 |
| % Hydrophobic | % Polar |
|---|---|
| 54.66 | 45.34 |
| According to VolSite | |
| HET Code: | PIL |
|---|---|
| Formula: | C18H18Cl2N2O3 |
| Molecular weight: | 381.253 g/mol |
| DrugBank ID: | DB01791 |
| Buried Surface Area: | 67.12 % |
| Polar Surface area: | 60.45 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 13.7802 | 5.74356 | 12.8316 |
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 |
| C24 | CG | MET- 273 | 4.48 | 0 | Hydrophobic |
| C19 | CG | MET- 273 | 3.98 | 0 | Hydrophobic |
| CL20 | SD | MET- 273 | 4.11 | 0 | Hydrophobic |
| CL20 | CB | ASP- 318 | 3.77 | 0 | Hydrophobic |
| CL20 | CD2 | LEU- 319 | 3.39 | 0 | Hydrophobic |
| C11 | CB | ASN- 321 | 4.13 | 0 | Hydrophobic |
| C11 | CE1 | TYR- 329 | 4.02 | 0 | Hydrophobic |
| C11 | CB | TRP- 332 | 4.1 | 0 | Hydrophobic |
| C11 | CB | THR- 333 | 4.33 | 0 | Hydrophobic |
| CL25 | CD1 | ILE- 336 | 4.31 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 336 | 4.23 | 0 | Hydrophobic |
| C12 | CG1 | ILE- 336 | 4.19 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 336 | 3.95 | 0 | Hydrophobic |
| C5 | CG1 | ILE- 336 | 4.38 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 336 | 4.32 | 0 | Hydrophobic |
| C1 | CG1 | ILE- 336 | 4.15 | 0 | Hydrophobic |
| C9 | CG2 | ILE- 336 | 3.71 | 0 | Hydrophobic |
| C6 | SD | MET- 337 | 3.81 | 0 | Hydrophobic |
| CL25 | CZ | PHE- 340 | 4.04 | 0 | Hydrophobic |
| C5 | CE2 | PHE- 340 | 3.42 | 0 | Hydrophobic |
| C5 | CE | MET- 357 | 4.21 | 0 | Hydrophobic |
| C7 | SD | MET- 357 | 3.68 | 0 | Hydrophobic |
| C7 | CB | SER- 368 | 3.86 | 0 | Hydrophobic |
| O10 | NE2 | GLN- 369 | 3.05 | 142.17 | H-Bond (Protein Donor) |
| O3 | NE2 | GLN- 369 | 3.16 | 143.9 | H-Bond (Protein Donor) |
| C4 | CG | PHE- 372 | 3.77 | 0 | Hydrophobic |
| C8 | CB | PHE- 372 | 3.77 | 0 | Hydrophobic |
| C2 | CE2 | PHE- 372 | 3.37 | 0 | Hydrophobic |
| N16 | O | HOH- 2010 | 2.94 | 151.77 | H-Bond (Ligand Donor) |
