sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.420 Å
X-ray
2010-07-28
| Name: | cAMP-specific 3',5'-cyclic phosphodiesterase 4B |
|---|---|
| ID: | PDE4B_HUMAN |
| AC: | Q07343 |
| 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: | 45.916 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.110 | 752.625 |
| % Hydrophobic | % Polar |
|---|---|
| 60.09 | 39.91 |
| According to VolSite | |
| HET Code: | ZG1 |
|---|---|
| Formula: | C21H28N7O3 |
| Molecular weight: | 426.492 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 51.92 % |
| Polar Surface area: | 112.45 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 48.0442 | 46.3834 | 64.197 |
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 |
| N4 | O | HOH- 5 | 2.78 | 152.37 | H-Bond (Protein Donor) |
| C1 | CE2 | TYR- 233 | 4.49 | 0 | Hydrophobic |
| C31 | CB | SER- 282 | 3.77 | 0 | Hydrophobic |
| C30 | CB | MET- 347 | 4.01 | 0 | Hydrophobic |
| C13 | CG | MET- 347 | 3.72 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 393 | 3.68 | 0 | Hydrophobic |
| C1 | CB | ASN- 395 | 3.84 | 0 | Hydrophobic |
| C2 | CG | PRO- 396 | 4.18 | 0 | Hydrophobic |
| C2 | CE1 | TYR- 403 | 3.86 | 0 | Hydrophobic |
| C1 | CB | TRP- 406 | 3.99 | 0 | Hydrophobic |
| C1 | CB | THR- 407 | 4.28 | 0 | Hydrophobic |
| C1 | CG2 | ILE- 410 | 4.32 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 410 | 4.05 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 410 | 3.29 | 0 | Hydrophobic |
| C10 | CZ | PHE- 414 | 4.35 | 0 | Hydrophobic |
| N17 | NE2 | GLN- 443 | 3.06 | 155.89 | H-Bond (Protein Donor) |
| C2 | CD2 | PHE- 446 | 4.37 | 0 | Hydrophobic |
| C14 | CZ | PHE- 446 | 3.88 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 446 | 3.52 | 0 | Aromatic Face/Face |
