sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.080 Å
X-ray
2012-12-05
| 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: | 25.834 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.040 | 506.250 |
| % Hydrophobic | % Polar |
|---|---|
| 65.33 | 34.67 |
| According to VolSite | |
| HET Code: | 5BA |
|---|---|
| Formula: | C23H32BrN4O3 |
| Molecular weight: | 492.429 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 49.71 % |
| Polar Surface area: | 75.44 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -43.7961 | 15.823 | 43.1801 |
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 |
| BR | CZ | TYR- 612 | 4.1 | 0 | Hydrophobic |
| CAC | CE2 | TYR- 612 | 3.67 | 0 | Hydrophobic |
| CAB | CD1 | LEU- 725 | 3.77 | 0 | Hydrophobic |
| CAB | CD2 | LEU- 765 | 3.89 | 0 | Hydrophobic |
| BR | CB | ALA- 767 | 4.48 | 0 | Hydrophobic |
| CAL | CG1 | VAL- 782 | 4.27 | 0 | Hydrophobic |
| BR | CG2 | VAL- 782 | 4.38 | 0 | Hydrophobic |
| CAL | CD1 | PHE- 786 | 4.11 | 0 | Hydrophobic |
| CAW | CE1 | PHE- 786 | 3.37 | 0 | Hydrophobic |
| CAL | SD | MET- 816 | 4.49 | 0 | Hydrophobic |
| CAI | CB | MET- 816 | 3.65 | 0 | Hydrophobic |
| NAS | OE1 | GLN- 817 | 2.86 | 174.36 | H-Bond (Ligand Donor) |
| OAF | NE2 | GLN- 817 | 2.96 | 174.46 | H-Bond (Protein Donor) |
| BR | CZ | PHE- 820 | 4.4 | 0 | Hydrophobic |
| CBC | CZ | PHE- 820 | 4.15 | 0 | Hydrophobic |
| CAB | CE1 | PHE- 820 | 3.92 | 0 | Hydrophobic |
| CAJ | CB | PHE- 820 | 3.6 | 0 | Hydrophobic |
