sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2007-12-03
| Name: | cGMP-specific 3',5'-cyclic phosphodiesterase |
|---|---|
| ID: | PDE5A_HUMAN |
| AC: | O76074 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 32.097 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.679 | 540.000 |
| % Hydrophobic | % Polar |
|---|---|
| 53.75 | 46.25 |
| According to VolSite | |
| HET Code: | WAN |
|---|---|
| Formula: | C15H19N5O4S2 |
| Molecular weight: | 397.472 g/mol |
| DrugBank ID: | DB08729 |
| Buried Surface Area: | 50.57 % |
| Polar Surface area: | 165.29 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 44.4492 | 15.4054 | 46.7865 |
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 |
| C21 | CZ | TYR- 612 | 4.45 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 765 | 4.07 | 0 | Hydrophobic |
| C21 | CB | ALA- 767 | 3.97 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 782 | 4.49 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 782 | 4.32 | 0 | Hydrophobic |
| C11 | CB | ALA- 783 | 3.64 | 0 | Hydrophobic |
| C25 | CZ | PHE- 786 | 3.55 | 0 | Hydrophobic |
| C11 | CE2 | PHE- 787 | 4.36 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 813 | 4.04 | 0 | Hydrophobic |
| S7 | CE | MET- 816 | 3.54 | 0 | Hydrophobic |
| C10 | CB | MET- 816 | 4.29 | 0 | Hydrophobic |
| O16 | NE2 | GLN- 817 | 3.12 | 170.01 | H-Bond (Protein Donor) |
| N14 | OE1 | GLN- 817 | 2.83 | 168.87 | H-Bond (Ligand Donor) |
| C24 | CZ | PHE- 820 | 4.29 | 0 | Hydrophobic |
| C21 | CE2 | PHE- 820 | 4.42 | 0 | Hydrophobic |
