sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2009-02-03
| 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 |
|---|---|
| C | 100 % |
| B-Factor: | 27.474 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.212 | 941.625 |
| % Hydrophobic | % Polar |
|---|---|
| 52.69 | 47.31 |
| According to VolSite | |
| HET Code: | ROF |
|---|---|
| Formula: | C17H14Cl2F2N2O3 |
| Molecular weight: | 403.207 g/mol |
| DrugBank ID: | DB01656 |
| Buried Surface Area: | 66.17 % |
| 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: | 7 |
| X | Y | Z |
|---|---|---|
| -17.8405 | 5.12065 | 35.208 |
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 |
| C5 | CG | MET- 439 | 3.9 | 0 | Hydrophobic |
| CL26 | SD | MET- 439 | 4.42 | 0 | Hydrophobic |
| C1 | CG | MET- 439 | 4.45 | 0 | Hydrophobic |
| CL26 | CB | ASP- 484 | 3.63 | 0 | Hydrophobic |
| CL26 | CD2 | LEU- 485 | 3.52 | 0 | Hydrophobic |
| F18 | CB | ASN- 487 | 3.46 | 0 | Hydrophobic |
| F18 | CG | PRO- 488 | 3.47 | 0 | Hydrophobic |
| F18 | CE1 | TYR- 495 | 3.34 | 0 | Hydrophobic |
| F17 | CB | TRP- 498 | 3.44 | 0 | Hydrophobic |
| F17 | CB | THR- 499 | 4.12 | 0 | Hydrophobic |
| C12 | CG2 | ILE- 502 | 3.83 | 0 | Hydrophobic |
| C20 | CG2 | ILE- 502 | 4.23 | 0 | Hydrophobic |
| CL25 | CD1 | ILE- 502 | 4.25 | 0 | Hydrophobic |
| F17 | CG2 | ILE- 502 | 3.82 | 0 | Hydrophobic |
| C13 | CG1 | ILE- 502 | 4.11 | 0 | Hydrophobic |
| C23 | CE2 | PHE- 506 | 4.21 | 0 | Hydrophobic |
| C20 | CE2 | PHE- 506 | 3.93 | 0 | Hydrophobic |
| CL25 | CZ | PHE- 506 | 4.01 | 0 | Hydrophobic |
| C23 | CG | MET- 523 | 3.47 | 0 | Hydrophobic |
| C22 | CB | SER- 534 | 3.32 | 0 | Hydrophobic |
| O15 | NE2 | GLN- 535 | 3.17 | 136.27 | H-Bond (Protein Donor) |
| O19 | NE2 | GLN- 535 | 3.28 | 155.48 | H-Bond (Protein Donor) |
| C22 | CB | PHE- 538 | 4.19 | 0 | Hydrophobic |
| C21 | CG | PHE- 538 | 4.07 | 0 | Hydrophobic |
| C13 | CE2 | PHE- 538 | 3.29 | 0 | Hydrophobic |
| F18 | CE2 | PHE- 538 | 3.83 | 0 | Hydrophobic |
