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
2011-01-26
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 36.622 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.068 | 796.500 |
| % Hydrophobic | % Polar |
|---|---|
| 58.90 | 41.10 |
| According to VolSite | |
| HET Code: | IBM |
|---|---|
| Formula: | C10H14N4O2 |
| Molecular weight: | 222.244 g/mol |
| DrugBank ID: | DB07954 |
| Buried Surface Area: | 47.22 % |
| Polar Surface area: | 69.3 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 75.5963 | 51.5024 | 41.6628 |
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 |
| C10 | CZ | PHE- 251 | 4.28 | 0 | Hydrophobic |
| C13 | CG | MET- 365 | 3.92 | 0 | Hydrophobic |
| C10 | CB | ILE- 403 | 4.23 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 420 | 4.2 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 420 | 4.42 | 0 | Hydrophobic |
| C11 | CZ | TYR- 424 | 4.12 | 0 | Hydrophobic |
| C14 | CE2 | TYR- 424 | 4.22 | 0 | Hydrophobic |
| C14 | CE1 | PHE- 441 | 3.66 | 0 | Hydrophobic |
| N7 | OE1 | GLU- 453 | 2.58 | 165.86 | H-Bond (Ligand Donor) |
| C10 | CE2 | PHE- 456 | 4.17 | 0 | Hydrophobic |
| C12 | CE1 | PHE- 456 | 3.56 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 456 | 3.64 | 0 | Aromatic Face/Face |
