sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.640 Å
X-ray
2013-09-23
| 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: | 52.958 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.280 | 907.875 |
| % Hydrophobic | % Polar |
|---|---|
| 59.48 | 40.52 |
| According to VolSite | |
| HET Code: | 2F4 |
|---|---|
| Formula: | C24H18F2N6O |
| Molecular weight: | 444.436 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.19 % |
| Polar Surface area: | 87.75 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -25.4932 | 47.469 | 20.1808 |
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 |
| C01 | CD2 | LEU- 625 | 3.59 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 665 | 3.91 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 668 | 3.53 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 682 | 3.75 | 0 | Hydrophobic |
| C17 | CG2 | ILE- 682 | 4.03 | 0 | Hydrophobic |
| N22 | OH | TYR- 683 | 2.68 | 174.63 | H-Bond (Protein Donor) |
| C01 | CZ | PHE- 686 | 4.33 | 0 | Hydrophobic |
| F27 | CB | PRO- 702 | 3.39 | 0 | Hydrophobic |
| C30 | CB | MET- 703 | 4.18 | 0 | Hydrophobic |
| C18 | CG | MET- 703 | 3.74 | 0 | Hydrophobic |
| C32 | SD | MET- 703 | 3.99 | 0 | Hydrophobic |
| F27 | CB | LYS- 708 | 3.8 | 0 | Hydrophobic |
| F27 | CB | GLU- 711 | 3.37 | 0 | Hydrophobic |
| C24 | CG2 | VAL- 712 | 3.75 | 0 | Hydrophobic |
| C01 | CE1 | PHE- 719 | 4.47 | 0 | Hydrophobic |
| C32 | CD1 | PHE- 719 | 3.29 | 0 | Hydrophobic |
