sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2013-08-12
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.550 | 5.780 | 5.780 | 0.220 | 6.000 | 2 |
| Name: | cGMP-dependent 3',5'-cyclic phosphodiesterase |
|---|---|
| ID: | PDE2A_HUMAN |
| AC: | O00408 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.1.4.17 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 23.642 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.164 | 897.750 |
| % Hydrophobic | % Polar |
|---|---|
| 58.27 | 41.73 |
| According to VolSite | |
| HET Code: | EH9 |
|---|---|
| Formula: | C14H23N5O |
| Molecular weight: | 277.365 g/mol |
| DrugBank ID: | DB07711 |
| Buried Surface Area: | 58.39 % |
| Polar Surface area: | 89.85 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 22.3145 | -25.3339 | 7.2238 |
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 |
| C40 | CE2 | TYR- 655 | 3.84 | 0 | Hydrophobic |
| C28 | CB | LEU- 770 | 4.26 | 0 | Hydrophobic |
| C30 | CD1 | LEU- 770 | 4.09 | 0 | Hydrophobic |
| C34 | CB | HIS- 773 | 3.86 | 0 | Hydrophobic |
| C34 | CB | THR- 805 | 4.46 | 0 | Hydrophobic |
| C34 | CD1 | LEU- 809 | 4.35 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 809 | 4.08 | 0 | Hydrophobic |
| C40 | CG2 | ILE- 826 | 4.2 | 0 | Hydrophobic |
| C40 | CZ | PHE- 830 | 3.92 | 0 | Hydrophobic |
| N6 | NE2 | GLN- 859 | 2.92 | 159.82 | H-Bond (Protein Donor) |
| N24 | OE1 | GLN- 859 | 2.87 | 167.3 | H-Bond (Ligand Donor) |
| C26 | CE1 | PHE- 862 | 4.3 | 0 | Hydrophobic |
| C34 | CG2 | ILE- 866 | 4.06 | 0 | Hydrophobic |
| C30 | CG2 | ILE- 866 | 4.01 | 0 | Hydrophobic |
| C34 | CD1 | ILE- 870 | 3.55 | 0 | Hydrophobic |
