sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2013-09-27
| 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: | 12.677 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.557 | 1110.375 |
| % Hydrophobic | % Polar |
|---|---|
| 58.66 | 41.34 |
| According to VolSite | |
| HET Code: | 19T |
|---|---|
| Formula: | C19H17ClN3O2S |
| Molecular weight: | 386.875 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.34 % |
| Polar Surface area: | 106.18 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -16.1889 | 34.3537 | -6.88296 |
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 |
| C14 | CZ | TYR- 405 | 3.88 | 0 | Hydrophobic |
| C19 | CG | MET- 519 | 3.72 | 0 | Hydrophobic |
| C22 | CE | MET- 519 | 4.19 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 565 | 4.42 | 0 | Hydrophobic |
| C15 | CB | ASN- 567 | 4.02 | 0 | Hydrophobic |
| C13 | CE1 | TYR- 575 | 4.04 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 582 | 4.14 | 0 | Hydrophobic |
| C17 | CG1 | ILE- 582 | 4.44 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 582 | 3.99 | 0 | Hydrophobic |
| C5 | CG2 | ILE- 582 | 3.77 | 0 | Hydrophobic |
| CL1 | CG | MET- 603 | 3.36 | 0 | Hydrophobic |
| N3 | NE2 | GLN- 615 | 3.12 | 174.13 | H-Bond (Protein Donor) |
| C15 | CE2 | PHE- 618 | 4.16 | 0 | Hydrophobic |
| C13 | CE2 | PHE- 618 | 3.91 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 618 | 3.93 | 0 | Aromatic Face/Face |
| CL1 | CD1 | LEU- 674 | 3.74 | 0 | Hydrophobic |
| C19 | CD | LYS- 677 | 4.45 | 0 | Hydrophobic |
| S8 | CD | LYS- 677 | 4.15 | 0 | Hydrophobic |
| CL1 | CD | LYS- 677 | 3.78 | 0 | Hydrophobic |
| N16 | O | HOH- 808 | 3.28 | 150.84 | H-Bond (Ligand Donor) |
