sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.070 Å
X-ray
2012-01-18
| 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: | 28.243 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.063 | 671.625 |
| % Hydrophobic | % Polar |
|---|---|
| 62.81 | 37.19 |
| According to VolSite | |
| HET Code: | 0JQ |
|---|---|
| Formula: | C24H30N4O3 |
| Molecular weight: | 422.520 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 41.43 % |
| Polar Surface area: | 80.6 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -28.0909 | 50.8106 | 19.6816 |
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 |
| C16 | CB | SER- 561 | 4.12 | 0 | Hydrophobic |
| O3 | OG | SER- 563 | 3.4 | 163.16 | H-Bond (Ligand Donor) |
| C8 | CD2 | LEU- 625 | 4.15 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 668 | 3.82 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 682 | 4.01 | 0 | Hydrophobic |
| C9 | CG2 | ILE- 682 | 4.3 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 682 | 3.99 | 0 | Hydrophobic |
| C10 | CE2 | PHE- 686 | 4.37 | 0 | Hydrophobic |
| C16 | CE1 | PHE- 686 | 4.08 | 0 | Hydrophobic |
| C12 | CZ | PHE- 686 | 3.44 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 701 | 4.3 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 701 | 3.51 | 0 | Hydrophobic |
| C10 | SD | MET- 703 | 3.67 | 0 | Hydrophobic |
| C13 | CE | MET- 703 | 3.99 | 0 | Hydrophobic |
| C24 | CE | MET- 703 | 3.75 | 0 | Hydrophobic |
| C16 | CE | MET- 704 | 4.14 | 0 | Hydrophobic |
| O2 | NE2 | GLN- 716 | 2.85 | 161.31 | H-Bond (Protein Donor) |
| C11 | CE2 | PHE- 719 | 4.35 | 0 | Hydrophobic |
| C10 | CG | PHE- 719 | 3.73 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 719 | 3.72 | 0 | Aromatic Face/Face |
