sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2003-07-09
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.000 | 9.000 | 9.000 | 0.000 | 9.000 | 1 |
| 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: | 30.980 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.263 | 995.625 |
| % Hydrophobic | % Polar |
|---|---|
| 59.32 | 40.68 |
| According to VolSite | |
| HET Code: | VDN |
|---|---|
| Formula: | C23H33N6O4S |
| Molecular weight: | 489.611 g/mol |
| DrugBank ID: | DB00862 |
| Buried Surface Area: | 47.2 % |
| Polar Surface area: | 118.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 1.84888 | 67.9544 | 83.3957 |
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 |
| C31 | CZ | TYR- 612 | 3.94 | 0 | Hydrophobic |
| C34 | CE2 | TYR- 612 | 4.42 | 0 | Hydrophobic |
| C15 | CE2 | TYR- 664 | 4.49 | 0 | Hydrophobic |
| C19 | CZ | TYR- 664 | 3.89 | 0 | Hydrophobic |
| C31 | CB | ALA- 767 | 4.25 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 782 | 4.05 | 0 | Hydrophobic |
| C31 | CG2 | VAL- 782 | 4.34 | 0 | Hydrophobic |
| C1 | CB | ALA- 783 | 3.79 | 0 | Hydrophobic |
| C2 | CD2 | PHE- 786 | 4.46 | 0 | Hydrophobic |
| C33 | CZ | PHE- 786 | 3.56 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 804 | 3.45 | 0 | Hydrophobic |
| C2 | CB | ILE- 813 | 4.42 | 0 | Hydrophobic |
| C5 | CB | MET- 816 | 3.54 | 0 | Hydrophobic |
| N22 | NE2 | GLN- 817 | 2.82 | 158.8 | H-Bond (Protein Donor) |
| O27 | OE1 | GLN- 817 | 3 | 166.14 | H-Bond (Ligand Donor) |
| C15 | CB | PHE- 820 | 4.38 | 0 | Hydrophobic |
| C32 | CZ | PHE- 820 | 4.33 | 0 | Hydrophobic |
| C8 | CB | PHE- 820 | 3.95 | 0 | Hydrophobic |
