sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.260 Å
X-ray
2013-09-04
| 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: | 47.779 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.068 | 992.250 |
| % Hydrophobic | % Polar |
|---|---|
| 53.74 | 46.26 |
| According to VolSite | |
| HET Code: | P98 |
|---|---|
| Formula: | C26H23N3O |
| Molecular weight: | 393.480 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.6 % |
| Polar Surface area: | 39.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 5 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 21.0755 | 25.333 | 41.0018 |
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 |
| C29 | CE2 | TYR- 524 | 4.34 | 0 | Hydrophobic |
| C30 | CD2 | LEU- 675 | 3.61 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 678 | 3.64 | 0 | Hydrophobic |
| C24 | CB | ALA- 689 | 3.98 | 0 | Hydrophobic |
| C23 | CG2 | ILE- 692 | 3.58 | 0 | Hydrophobic |
| C29 | CG2 | ILE- 692 | 4.2 | 0 | Hydrophobic |
| C6 | CZ | TYR- 693 | 4.39 | 0 | Hydrophobic |
| C29 | CZ | PHE- 696 | 4.34 | 0 | Hydrophobic |
| C15 | CB | PRO- 712 | 3.73 | 0 | Hydrophobic |
| C13 | CB | MET- 713 | 4.45 | 0 | Hydrophobic |
| C10 | CE | MET- 713 | 4.23 | 0 | Hydrophobic |
| C2 | CE | MET- 713 | 3.65 | 0 | Hydrophobic |
| C6 | CE | MET- 713 | 4.43 | 0 | Hydrophobic |
| C11 | CB | MET- 713 | 3.94 | 0 | Hydrophobic |
| C1 | CE | MET- 713 | 3.81 | 0 | Hydrophobic |
| C15 | CB | LYS- 718 | 4.1 | 0 | Hydrophobic |
| C15 | CB | GLU- 721 | 3.5 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 722 | 3.76 | 0 | Hydrophobic |
| C6 | CB | PHE- 729 | 4.5 | 0 | Hydrophobic |
| C2 | CB | PHE- 729 | 3.84 | 0 | Hydrophobic |
| C30 | CZ | PHE- 729 | 4.05 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 729 | 3.77 | 0 | Aromatic Face/Face |
