sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.450 Å
X-ray
2013-03-25
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 20.920 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.949 | 860.625 |
| % Hydrophobic | % Polar |
|---|---|
| 66.27 | 33.73 |
| According to VolSite | |
| HET Code: | 1M1 |
|---|---|
| Formula: | C19H14N4 |
| Molecular weight: | 298.341 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.95 % |
| Polar Surface area: | 42.74 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 18.2044 | -2.23257 | -15.7593 |
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 |
| CAG | CD1 | LEU- 22 | 4.06 | 0 | Hydrophobic |
| CAF | CG2 | VAL- 49 | 4.22 | 0 | Hydrophobic |
| CAI | CG1 | ILE- 53 | 4.38 | 0 | Hydrophobic |
| CAF | CG2 | ILE- 53 | 3.97 | 0 | Hydrophobic |
| CAH | CD1 | ILE- 53 | 3.58 | 0 | Hydrophobic |
| CAJ | CD2 | LEU- 54 | 3.91 | 0 | Hydrophobic |
| CAU | CG2 | VAL- 59 | 3.88 | 0 | Hydrophobic |
| CAH | CG2 | VAL- 59 | 4.18 | 0 | Hydrophobic |
| CAL | CG1 | VAL- 80 | 3.71 | 0 | Hydrophobic |
| CAM | CD1 | LEU- 87 | 4.08 | 0 | Hydrophobic |
| CAN | CG | GLU- 88 | 4.4 | 0 | Hydrophobic |
| CAQ | CZ2 | TRP- 90 | 3.91 | 0 | Hydrophobic |
| CAS | CG2 | ILE- 109 | 3.81 | 0 | Hydrophobic |
| CAU | CB | ALA- 111 | 3.86 | 0 | Hydrophobic |
| CAQ | CE | MET- 117 | 4.32 | 0 | Hydrophobic |
| CAO | CE | MET- 117 | 3.65 | 0 | Hydrophobic |
| CAN | SD | MET- 117 | 3.52 | 0 | Hydrophobic |
| CAL | CD1 | LEU- 123 | 4.05 | 0 | Hydrophobic |
| CAL | CG2 | VAL- 127 | 4.26 | 0 | Hydrophobic |
| CAF | CD1 | LEU- 147 | 3.69 | 0 | Hydrophobic |
| NAB | OH | TYR- 149 | 2.74 | 163.34 | H-Bond (Protein Donor) |
| NAP | O | HOH- 322 | 3.11 | 157.97 | H-Bond (Ligand Donor) |
