sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2007-02-15
| Name: | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A |
|---|---|
| ID: | PDE10_RAT |
| AC: | Q9QYJ6 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | 3.1.4.17 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 22.194 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.914 | 621.000 |
| % Hydrophobic | % Polar |
|---|---|
| 56.52 | 43.48 |
| According to VolSite | |
| HET Code: | PFH |
|---|---|
| Formula: | C24H23N3O3 |
| Molecular weight: | 401.458 g/mol |
| DrugBank ID: | DB08389 |
| Buried Surface Area: | 46.65 % |
| Polar Surface area: | 56.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 0 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 12.3881 | 20.0088 | 43.0702 |
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 |
| C19 | CD2 | LEU- 625 | 4.28 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 625 | 4.33 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 625 | 4.14 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 668 | 3.3 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 682 | 4.08 | 0 | Hydrophobic |
| C1 | CG2 | ILE- 682 | 4.32 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 682 | 4.04 | 0 | Hydrophobic |
| C14 | CZ | TYR- 683 | 4.43 | 0 | Hydrophobic |
| C19 | CZ | PHE- 686 | 4.36 | 0 | Hydrophobic |
| C14 | CE2 | PHE- 686 | 4.3 | 0 | Hydrophobic |
| C16 | SD | MET- 703 | 4.17 | 0 | Hydrophobic |
| C14 | SD | MET- 703 | 3.79 | 0 | Hydrophobic |
| C24 | SD | MET- 703 | 4.44 | 0 | Hydrophobic |
| C17 | CE | MET- 703 | 4.07 | 0 | Hydrophobic |
| O11 | NE2 | GLN- 716 | 3.37 | 156.89 | H-Bond (Protein Donor) |
| C16 | CE1 | PHE- 719 | 3.93 | 0 | Hydrophobic |
| C14 | CB | PHE- 719 | 4.08 | 0 | Hydrophobic |
| C12 | CE2 | PHE- 719 | 4.06 | 0 | Hydrophobic |
| C29 | CB | PHE- 719 | 4.12 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 719 | 3.79 | 0 | Aromatic Face/Face |
| C27 | CB | ALA- 722 | 3.73 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 723 | 3.82 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 723 | 3.58 | 0 | Hydrophobic |
