sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.720 Å
X-ray
2009-09-10
| 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: | 48.403 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.049 | 742.500 |
| % Hydrophobic | % Polar |
|---|---|
| 57.27 | 42.73 |
| According to VolSite | |
| HET Code: | WTC |
|---|---|
| Formula: | C17H18N4O |
| Molecular weight: | 294.351 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 54.53 % |
| Polar Surface area: | 59.28 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 98.1657 | 22.515 | 10.9754 |
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 | CE2 | PHE- 251 | 4.46 | 0 | Hydrophobic |
| C12 | CG | MET- 365 | 3.66 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 403 | 4.09 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 417 | 3.96 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 420 | 4.23 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 420 | 3.6 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 420 | 3.59 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 421 | 3.62 | 0 | Hydrophobic |
| C21 | CG | LEU- 421 | 4.06 | 0 | Hydrophobic |
| C14 | CZ | TYR- 424 | 4.39 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 447 | 4.37 | 0 | Hydrophobic |
| C19 | CB | ALA- 452 | 3.85 | 0 | Hydrophobic |
| N7 | OE1 | GLN- 453 | 2.64 | 161.13 | H-Bond (Ligand Donor) |
| O15 | NE2 | GLN- 453 | 3.34 | 160.69 | H-Bond (Protein Donor) |
| C11 | CE1 | PHE- 456 | 4.4 | 0 | Hydrophobic |
| C16 | CD1 | PHE- 456 | 3.67 | 0 | Hydrophobic |
