sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.870 Å
X-ray
2013-03-25
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.540 | 5.580 | 5.580 | 0.040 | 5.620 | 2 |
| 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: | 30.669 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 2.148 | 850.500 |
| % Hydrophobic | % Polar |
|---|---|
| 73.81 | 26.19 |
| According to VolSite | |
| HET Code: | 18F |
|---|---|
| Formula: | C20H16N2 |
| Molecular weight: | 284.354 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.43 % |
| Polar Surface area: | 17.82 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 19.0511 | -17.2555 | 12.8676 |
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- 17 | 3.7 | 0 | Hydrophobic |
| CAF | SD | MET- 20 | 3.85 | 0 | Hydrophobic |
| CAV | CE | MET- 20 | 3.66 | 0 | Hydrophobic |
| CAH | CE | MET- 20 | 3.91 | 0 | Hydrophobic |
| CAO | CD1 | LEU- 22 | 4.28 | 0 | Hydrophobic |
| CAU | CD1 | LEU- 22 | 3.95 | 0 | Hydrophobic |
| CAH | CB | LEU- 38 | 3.96 | 0 | Hydrophobic |
| CAU | CD1 | LEU- 38 | 3.77 | 0 | Hydrophobic |
| CAS | CB | ALA- 47 | 3.44 | 0 | Hydrophobic |
| CAT | CG1 | VAL- 49 | 4.39 | 0 | Hydrophobic |
| CAF | CD | ARG- 61 | 4.29 | 0 | Hydrophobic |
| NAB | NH1 | ARG- 61 | 2.9 | 139.29 | H-Bond (Protein Donor) |
| CAF | CD1 | LEU- 63 | 4.03 | 0 | Hydrophobic |
| NAB | NE2 | GLN- 78 | 2.83 | 155.85 | H-Bond (Protein Donor) |
| CAL | CD1 | ILE- 109 | 3.79 | 0 | Hydrophobic |
| CAP | CG2 | ILE- 129 | 3.82 | 0 | Hydrophobic |
| CAK | CG2 | ILE- 129 | 4.24 | 0 | Hydrophobic |
| CAN | CD1 | ILE- 129 | 3.77 | 0 | Hydrophobic |
| CAG | CG2 | THR- 131 | 4.49 | 0 | Hydrophobic |
| CAI | CG2 | VAL- 145 | 4.33 | 0 | Hydrophobic |
| CAR | CG1 | VAL- 145 | 3.71 | 0 | Hydrophobic |
| CAP | CG2 | VAL- 145 | 4.29 | 0 | Hydrophobic |
| CAS | CD2 | LEU- 147 | 3.97 | 0 | Hydrophobic |
