sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2012-11-02
| 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: | 22.862 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.204 | 887.625 |
| % Hydrophobic | % Polar |
|---|---|
| 55.89 | 44.11 |
| According to VolSite | |
| HET Code: | 19F |
|---|---|
| Formula: | C27H32N4O4 |
| Molecular weight: | 476.567 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.52 % |
| Polar Surface area: | 97.97 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| -15.6659 | 25.1993 | 23.6288 |
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 |
| CAD | CE2 | TYR- 655 | 3.7 | 0 | Hydrophobic |
| CAB | CD2 | LEU- 770 | 4.08 | 0 | Hydrophobic |
| CAP | CB | LEU- 770 | 4.04 | 0 | Hydrophobic |
| CAJ | CB | LEU- 770 | 3.51 | 0 | Hydrophobic |
| CAI | CD1 | LEU- 770 | 3.82 | 0 | Hydrophobic |
| CAG | CB | HIS- 773 | 3.74 | 0 | Hydrophobic |
| CAG | CG2 | THR- 805 | 3.96 | 0 | Hydrophobic |
| CAC | CD2 | LEU- 809 | 4.09 | 0 | Hydrophobic |
| CAO | CD2 | LEU- 809 | 3.9 | 0 | Hydrophobic |
| CAI | CD1 | LEU- 809 | 3.81 | 0 | Hydrophobic |
| OAE | NE2 | GLN- 812 | 2.93 | 126.58 | H-Bond (Protein Donor) |
| CAC | CG | GLN- 812 | 3.98 | 0 | Hydrophobic |
| CAR | CG2 | ILE- 826 | 4.24 | 0 | Hydrophobic |
| CAC | CD1 | ILE- 826 | 4.25 | 0 | Hydrophobic |
| CAD | CD1 | ILE- 826 | 3.99 | 0 | Hydrophobic |
| CAR | CZ | TYR- 827 | 4.31 | 0 | Hydrophobic |
| CAR | CE2 | PHE- 830 | 3.53 | 0 | Hydrophobic |
| CBG | CZ | PHE- 830 | 3.84 | 0 | Hydrophobic |
| CAB | CE | MET- 847 | 4.21 | 0 | Hydrophobic |
| CAA | CE | MET- 847 | 4.47 | 0 | Hydrophobic |
| CBC | CE | MET- 847 | 3.46 | 0 | Hydrophobic |
| CAN | SD | MET- 847 | 3.62 | 0 | Hydrophobic |
| NAU | NE2 | GLN- 859 | 2.98 | 169.84 | H-Bond (Protein Donor) |
| OAE | OE1 | GLN- 859 | 3.03 | 171.76 | H-Bond (Ligand Donor) |
| CAA | CB | SER- 861 | 3.96 | 0 | Hydrophobic |
| CAR | CD1 | PHE- 862 | 4.33 | 0 | Hydrophobic |
| CAC | CE2 | PHE- 862 | 4.03 | 0 | Hydrophobic |
| CAO | CE1 | PHE- 862 | 4.02 | 0 | Hydrophobic |
| CAL | CB | PHE- 862 | 3.6 | 0 | Hydrophobic |
| CBB | CD1 | ILE- 866 | 4.45 | 0 | Hydrophobic |
| CAK | CG2 | ILE- 866 | 3.45 | 0 | Hydrophobic |
| CAI | CD1 | ILE- 870 | 3.74 | 0 | Hydrophobic |
