sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2012-07-13
| 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: | 35.226 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.119 | 631.125 |
| % Hydrophobic | % Polar |
|---|---|
| 57.75 | 42.25 |
| According to VolSite | |
| HET Code: | NI5 |
|---|---|
| Formula: | C21H29N4O4S |
| Molecular weight: | 433.544 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 48.03 % |
| Polar Surface area: | 100.89 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 35.6675 | -30.7563 | -41.7479 |
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 |
| CAJ | CZ | TYR- 612 | 4.29 | 0 | Hydrophobic |
| CAQ | CD1 | LEU- 725 | 3.92 | 0 | Hydrophobic |
| CAL | CD2 | LEU- 765 | 4.19 | 0 | Hydrophobic |
| CAM | CB | ALA- 767 | 3.94 | 0 | Hydrophobic |
| CAA | CB | ALA- 779 | 3.94 | 0 | Hydrophobic |
| CAM | CG2 | VAL- 782 | 4.25 | 0 | Hydrophobic |
| CAI | CG1 | VAL- 782 | 3.88 | 0 | Hydrophobic |
| CAI | CB | ALA- 783 | 4.09 | 0 | Hydrophobic |
| CAW | CE2 | PHE- 786 | 3.48 | 0 | Hydrophobic |
| CAK | CD2 | PHE- 786 | 3.99 | 0 | Hydrophobic |
| CAA | CG2 | ILE- 813 | 4.2 | 0 | Hydrophobic |
| CAG | CB | MET- 816 | 4.24 | 0 | Hydrophobic |
| CAK | CE | MET- 816 | 4.18 | 0 | Hydrophobic |
| CAA | CG | GLN- 817 | 4.32 | 0 | Hydrophobic |
| OAC | NE2 | GLN- 817 | 2.65 | 162.91 | H-Bond (Protein Donor) |
| NAS | OE1 | GLN- 817 | 2.81 | 159.21 | H-Bond (Ligand Donor) |
| CAH | CB | PHE- 820 | 3.73 | 0 | Hydrophobic |
| CAL | CZ | PHE- 820 | 4.12 | 0 | Hydrophobic |
