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
2009-09-11
| Name: | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A |
|---|---|
| ID: | PDE9A_HUMAN |
| AC: | O76083 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 41.323 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.084 | 803.250 |
| % Hydrophobic | % Polar |
|---|---|
| 50.42 | 49.58 |
| According to VolSite | |
| HET Code: | JAR |
|---|---|
| Formula: | C20H26N5O |
| Molecular weight: | 352.453 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 48.59 % |
| Polar Surface area: | 63.72 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 96.4742 | 21.4921 | 12.1552 |
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 |
| C1 | CE2 | PHE- 251 | 4.33 | 0 | Hydrophobic |
| C3 | CG | MET- 365 | 3.82 | 0 | Hydrophobic |
| C22 | CE | MET- 365 | 4.46 | 0 | Hydrophobic |
| C3 | CG2 | ILE- 403 | 3.9 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 420 | 4 | 0 | Hydrophobic |
| C28 | CD2 | LEU- 420 | 3.88 | 0 | Hydrophobic |
| C28 | CD2 | LEU- 421 | 4.06 | 0 | Hydrophobic |
| C26 | CE2 | TYR- 424 | 3.9 | 0 | Hydrophobic |
| C28 | CB | ALA- 452 | 3.89 | 0 | Hydrophobic |
| O9 | NE2 | GLN- 453 | 3.19 | 165.44 | H-Bond (Protein Donor) |
| N10 | OE1 | GLN- 453 | 2.67 | 167.39 | H-Bond (Ligand Donor) |
| C3 | CZ | PHE- 456 | 4.18 | 0 | Hydrophobic |
| C14 | CG | PHE- 456 | 4.03 | 0 | Hydrophobic |
