sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.140 Å
X-ray
2014-01-14
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.840 | 5.840 | 5.840 | 0.000 | 5.840 | 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: | 35.101 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.113 | 806.625 |
| % Hydrophobic | % Polar |
|---|---|
| 59.83 | 40.17 |
| According to VolSite | |
| HET Code: | 5EO |
|---|---|
| Formula: | C20H29N4O4S |
| Molecular weight: | 421.534 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 47.01 % |
| 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: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 27.6153 | -18.4448 | 20.002 |
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 | 3.9 | 0 | Hydrophobic |
| CAQ | CD1 | LEU- 725 | 4.46 | 0 | Hydrophobic |
| CAA | CB | ALA- 779 | 3.96 | 0 | Hydrophobic |
| CAA | CG2 | VAL- 782 | 3.48 | 0 | Hydrophobic |
| CAK | CB | ALA- 783 | 4.05 | 0 | Hydrophobic |
| CAB | CZ | PHE- 786 | 4.28 | 0 | Hydrophobic |
| CAM | CD2 | PHE- 786 | 4.08 | 0 | Hydrophobic |
| CAW | CE2 | PHE- 786 | 3.38 | 0 | Hydrophobic |
| CAK | CE2 | PHE- 787 | 4.27 | 0 | Hydrophobic |
| CAA | CG2 | ILE- 813 | 4 | 0 | Hydrophobic |
| CAH | CB | MET- 816 | 3.88 | 0 | Hydrophobic |
| CAM | CE | MET- 816 | 3.88 | 0 | Hydrophobic |
| CAA | CG | GLN- 817 | 4.23 | 0 | Hydrophobic |
| OAD | NE2 | GLN- 817 | 2.81 | 164.95 | H-Bond (Protein Donor) |
| NAS | OE1 | GLN- 817 | 2.84 | 169.03 | H-Bond (Ligand Donor) |
| CAL | CZ | PHE- 820 | 4.38 | 0 | Hydrophobic |
| CAI | CB | PHE- 820 | 3.79 | 0 | Hydrophobic |
| CAQ | CD1 | ILE- 824 | 3.96 | 0 | Hydrophobic |
