sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 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: | 21.754 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.401 | 1022.625 |
| % Hydrophobic | % Polar |
|---|---|
| 55.12 | 44.88 |
| According to VolSite | |
| HET Code: | D71 |
|---|---|
| Formula: | C19H13N5O4 |
| Molecular weight: | 375.338 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 77.72 % |
| Polar Surface area: | 112.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 9.74207 | -1.12411 | -64.5721 |
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 |
| O50 | O | HOH- 31 | 3 | 158.26 | H-Bond (Protein Donor) |
| C39 | CE1 | PHE- 196 | 3.4 | 0 | Hydrophobic |
| C32 | CG2 | THR- 200 | 3.88 | 0 | Hydrophobic |
| C24 | CZ | PHE- 201 | 4.2 | 0 | Hydrophobic |
| C32 | CG | MET- 439 | 3.97 | 0 | Hydrophobic |
| C26 | SD | MET- 439 | 4.2 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 485 | 3.55 | 0 | Hydrophobic |
| C1 | CB | ASN- 487 | 3.88 | 0 | Hydrophobic |
| C6 | CB | TRP- 498 | 4.44 | 0 | Hydrophobic |
| C6 | CB | THR- 499 | 4.43 | 0 | Hydrophobic |
| C2 | CG2 | ILE- 502 | 4.41 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 502 | 4.13 | 0 | Hydrophobic |
| C43 | CG2 | ILE- 502 | 4.28 | 0 | Hydrophobic |
| C28 | CD1 | ILE- 502 | 4.25 | 0 | Hydrophobic |
| C42 | SD | MET- 503 | 3.89 | 0 | Hydrophobic |
| C41 | CG | MET- 523 | 3.63 | 0 | Hydrophobic |
| C41 | CB | SER- 534 | 3.58 | 0 | Hydrophobic |
| N4 | NE2 | GLN- 535 | 3.06 | 138.43 | H-Bond (Protein Donor) |
| C39 | CB | PHE- 538 | 3.68 | 0 | Hydrophobic |
| C24 | CZ | PHE- 538 | 4.03 | 0 | Hydrophobic |
