sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2012-09-28
| Name: | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A |
|---|---|
| ID: | PDE10_HUMAN |
| AC: | Q9Y233 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.1.4.17 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 48.231 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.127 | 695.250 |
| % Hydrophobic | % Polar |
|---|---|
| 57.77 | 42.23 |
| According to VolSite | |
| HET Code: | LKF |
|---|---|
| Formula: | C18H24N6O2 |
| Molecular weight: | 356.422 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 45.91 % |
| Polar Surface area: | 69.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -16.4927 | -38.045 | 20.9413 |
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 |
| CAL | CZ | TYR- 514 | 3.94 | 0 | Hydrophobic |
| CAO | CE1 | TYR- 514 | 3.81 | 0 | Hydrophobic |
| CAY | CE2 | PHE- 629 | 3.5 | 0 | Hydrophobic |
| CAO | CB | SER- 667 | 3.91 | 0 | Hydrophobic |
| CAM | CG1 | VAL- 668 | 4.07 | 0 | Hydrophobic |
| CAO | CG2 | THR- 678 | 4.01 | 0 | Hydrophobic |
| CAN | CG2 | ILE- 682 | 4.18 | 0 | Hydrophobic |
| CAL | CD1 | ILE- 682 | 3.65 | 0 | Hydrophobic |
| CAP | CZ | TYR- 683 | 4.21 | 0 | Hydrophobic |
| CAP | CE2 | PHE- 686 | 4.28 | 0 | Hydrophobic |
| CAP | SD | MET- 703 | 3.87 | 0 | Hydrophobic |
| CAV | CE | MET- 703 | 4.43 | 0 | Hydrophobic |
| CAM | CE2 | PHE- 719 | 3.71 | 0 | Hydrophobic |
| CAP | CD1 | PHE- 719 | 4.02 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 719 | 3.65 | 0 | Aromatic Face/Face |
