sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 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: | 32.346 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.074 | 712.125 |
| % Hydrophobic | % Polar |
|---|---|
| 58.77 | 41.23 |
| According to VolSite | |
| HET Code: | ZG2 |
|---|---|
| Formula: | C29H35N6O3 |
| Molecular weight: | 515.627 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.22 % |
| Polar Surface area: | 99.56 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 6 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 48.2589 | 47.5384 | 65.206 |
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 | 2.86 | 155 | H-Bond (Protein Donor) |
| C39 | CB | SER- 282 | 3.56 | 0 | Hydrophobic |
| C11 | CG | MET- 347 | 4.5 | 0 | Hydrophobic |
| C13 | CG | MET- 347 | 3.61 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 393 | 3.44 | 0 | Hydrophobic |
| C2 | CB | ASN- 395 | 4.02 | 0 | Hydrophobic |
| C2 | CG | PRO- 396 | 3.98 | 0 | Hydrophobic |
| C2 | CE1 | TYR- 403 | 3.97 | 0 | Hydrophobic |
| C1 | CB | TRP- 406 | 4.29 | 0 | Hydrophobic |
| C1 | CB | THR- 407 | 4.37 | 0 | Hydrophobic |
| C1 | CG2 | ILE- 410 | 3.88 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 410 | 4.22 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 410 | 3.5 | 0 | Hydrophobic |
| C36 | SD | MET- 431 | 3.42 | 0 | Hydrophobic |
| N20 | NE2 | GLN- 443 | 3.31 | 158.86 | H-Bond (Protein Donor) |
| DuAr | DuAr | PHE- 446 | 3.6 | 0 | Aromatic Face/Face |
| C14 | CZ | PHE- 446 | 3.88 | 0 | Hydrophobic |
| C37 | CB | PHE- 446 | 4.15 | 0 | Hydrophobic |
| C35 | CB | TYR- 449 | 4.4 | 0 | Hydrophobic |
