sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2008-05-12
| 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: | 23.441 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.205 | 688.500 |
| % Hydrophobic | % Polar |
|---|---|
| 62.25 | 37.75 |
| According to VolSite | |
| HET Code: | 20A |
|---|---|
| Formula: | C21H26N5O2 |
| Molecular weight: | 380.463 g/mol |
| DrugBank ID: | DB06909 |
| Buried Surface Area: | 51.78 % |
| Polar Surface area: | 82.32 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 46.9854 | 47.3584 | 64.7941 |
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 |
| C16 | CG | MET- 347 | 3.71 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 393 | 3.53 | 0 | Hydrophobic |
| C17 | CB | ASN- 395 | 3.87 | 0 | Hydrophobic |
| C17 | CG | PRO- 396 | 4.08 | 0 | Hydrophobic |
| C17 | CE1 | TYR- 403 | 4.05 | 0 | Hydrophobic |
| C21 | CB | TRP- 406 | 4.08 | 0 | Hydrophobic |
| C21 | CB | THR- 407 | 4.39 | 0 | Hydrophobic |
| C21 | CG2 | ILE- 410 | 3.91 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 410 | 4.26 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 410 | 3.48 | 0 | Hydrophobic |
| C15 | CZ | PHE- 414 | 4.31 | 0 | Hydrophobic |
| C25 | SD | MET- 431 | 3.22 | 0 | Hydrophobic |
| C22 | CE | MET- 431 | 3.26 | 0 | Hydrophobic |
| N11 | NE2 | GLN- 443 | 3.17 | 164.75 | H-Bond (Protein Donor) |
| DuAr | DuAr | PHE- 446 | 3.57 | 0 | Aromatic Face/Face |
| C27 | CB | PHE- 446 | 3.82 | 0 | Hydrophobic |
| C16 | CZ | PHE- 446 | 4.06 | 0 | Hydrophobic |
| N12 | O | HOH- 511 | 2.93 | 156.83 | H-Bond (Protein Donor) |
