2.860 Å
X-ray
2002-08-04
| Name: | cGMP-dependent 3',5'-cyclic phosphodiesterase |
|---|---|
| ID: | PDE2A_MOUSE |
| AC: | Q922S4 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 90.383 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.612 | 273.375 |
| % Hydrophobic | % Polar |
|---|---|
| 61.73 | 38.27 |
| According to VolSite | |

| HET Code: | PCG |
|---|---|
| Formula: | C10H11N5O7P |
| Molecular weight: | 344.197 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 81.72 % |
| Polar Surface area: | 183.16 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 127.773 | 57.2502 | 118.275 |
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 |
| O2' | O | HOH- 2 | 2.91 | 179.99 | H-Bond (Protein Donor) |
| N7 | OG | SER- 424 | 2.68 | 159.03 | H-Bond (Protein Donor) |
| O6 | N | ASP- 439 | 2.75 | 154.65 | H-Bond (Protein Donor) |
| N1 | OD1 | ASP- 439 | 2.6 | 166.44 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 439 | 3.4 | 127.64 | H-Bond (Ligand Donor) |
| C5' | CD1 | ILE- 452 | 4.1 | 0 | Hydrophobic |
| O2A | N | ILE- 458 | 2.52 | 156.42 | H-Bond (Protein Donor) |
| C2' | CE1 | PHE- 480 | 4.48 | 0 | Hydrophobic |
| O1A | N | TYR- 481 | 2.96 | 130.17 | H-Bond (Protein Donor) |
| C5' | CD2 | TYR- 481 | 4.41 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 484 | 3.85 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 484 | 3.42 | 0 | Hydrophobic |
| C2' | CG2 | THR- 492 | 4.4 | 0 | Hydrophobic |
| O2' | OG1 | THR- 492 | 2.75 | 164.52 | H-Bond (Ligand Donor) |
| C2' | CD1 | ILE- 495 | 4.04 | 0 | Hydrophobic |