sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.440 Å
X-ray
2014-01-14
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.820 | 6.820 | 6.820 | 0.000 | 6.820 | 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: | 24.281 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.071 | 594.000 |
| % Hydrophobic | % Polar |
|---|---|
| 61.36 | 38.64 |
| According to VolSite | |
| HET Code: | 5IO |
|---|---|
| Formula: | C20H28IN4O4S |
| Molecular weight: | 547.430 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 53.11 % |
| Polar Surface area: | 100.89 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: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -29.3808 | 14.754 | -19.6966 |
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 |
| CAB | CE1 | TYR- 612 | 4.21 | 0 | Hydrophobic |
| IAG | CZ | TYR- 612 | 4.41 | 0 | Hydrophobic |
| CAQ | CD1 | LEU- 725 | 4.34 | 0 | Hydrophobic |
| CAL | CD2 | LEU- 765 | 3.9 | 0 | Hydrophobic |
| IAG | CB | ALA- 767 | 3.96 | 0 | Hydrophobic |
| CAA | CB | ALA- 779 | 3.84 | 0 | Hydrophobic |
| CAA | CG2 | VAL- 782 | 3.54 | 0 | Hydrophobic |
| CAV | CG2 | VAL- 782 | 4.23 | 0 | Hydrophobic |
| CAK | CB | ALA- 783 | 3.73 | 0 | Hydrophobic |
| CAM | CD2 | PHE- 786 | 4.49 | 0 | Hydrophobic |
| CAP | CE2 | PHE- 786 | 4.2 | 0 | Hydrophobic |
| CAM | CE2 | PHE- 787 | 4.37 | 0 | Hydrophobic |
| CAK | CG2 | ILE- 813 | 4.05 | 0 | Hydrophobic |
| CAM | CE | MET- 816 | 3.9 | 0 | Hydrophobic |
| CAI | CB | MET- 816 | 4.15 | 0 | Hydrophobic |
| CAA | CG | GLN- 817 | 4.26 | 0 | Hydrophobic |
| OAD | NE2 | GLN- 817 | 2.95 | 163.74 | H-Bond (Protein Donor) |
| NAS | OE1 | GLN- 817 | 3.29 | 158.99 | H-Bond (Ligand Donor) |
| IAG | CE2 | PHE- 820 | 4.31 | 0 | Hydrophobic |
| CAL | CZ | PHE- 820 | 3.83 | 0 | Hydrophobic |
| CAJ | CB | PHE- 820 | 3.93 | 0 | Hydrophobic |
