sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2011-07-27
| Name: | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta |
|---|---|
| ID: | PDE6D_HUMAN |
| AC: | O43924 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 100 % |
| B-Factor: | 27.935 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.442 | 830.250 |
| % Hydrophobic | % Polar |
|---|---|
| 59.76 | 40.24 |
| According to VolSite | |
| HET Code: | SER_SER_CMT_FAR |
|---|---|
| Formula: | C10H20N3O6S |
| Molecular weight: | 310.347 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.32 % |
| Polar Surface area: | 191.39 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 6 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 44.9641 | -14.2268 | 52.1714 |
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 |
| SG | CB | VAL- 59 | 4.01 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 59 | 3.96 | 0 | Hydrophobic |
| CB | CG1 | VAL- 80 | 3.56 | 0 | Hydrophobic |
| CB | CG | LEU- 87 | 3.6 | 0 | Hydrophobic |
| CB | CD2 | LEU- 87 | 4.26 | 0 | Hydrophobic |
| N | OE2 | GLU- 88 | 3.44 | 148.87 | H-Bond (Ligand Donor) |
| N | OE1 | GLU- 88 | 3.49 | 122.98 | H-Bond (Ligand Donor) |
| N | OE2 | GLU- 88 | 2.89 | 164.82 | H-Bond (Ligand Donor) |
| OG | OE2 | GLU- 88 | 2.9 | 152.07 | H-Bond (Ligand Donor) |
| N | OE2 | GLU- 88 | 3.44 | 0 | Ionic (Ligand Cationic) |
| N | OE1 | GLU- 88 | 3.49 | 0 | Ionic (Ligand Cationic) |
| CB | CZ2 | TRP- 90 | 3.96 | 0 | Hydrophobic |
| CB | CG1 | VAL- 127 | 4.33 | 0 | Hydrophobic |
