sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2009-04-02
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 49.515 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.892 | 708.750 |
| % Hydrophobic | % Polar |
|---|---|
| 55.71 | 44.29 |
| According to VolSite | |
| HET Code: | EV1 |
|---|---|
| Formula: | C20H21NO4 |
| Molecular weight: | 339.385 g/mol |
| DrugBank ID: | DB01113 |
| Buried Surface Area: | 51.19 % |
| Polar Surface area: | 49.81 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 0 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -5.3814 | -28.7306 | 35.5816 |
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 |
| C25 | CD2 | TYR- 524 | 3.67 | 0 | Hydrophobic |
| C23 | CB | SER- 571 | 4.17 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 635 | 3.78 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 635 | 3.75 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 675 | 3.74 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 678 | 4.42 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 692 | 4.22 | 0 | Hydrophobic |
| C17 | CG2 | ILE- 692 | 3.94 | 0 | Hydrophobic |
| C25 | CE1 | PHE- 696 | 3.57 | 0 | Hydrophobic |
| C23 | CE1 | PHE- 696 | 3.86 | 0 | Hydrophobic |
| C16 | CZ | PHE- 696 | 3.48 | 0 | Hydrophobic |
| C19 | SD | MET- 713 | 3.93 | 0 | Hydrophobic |
| C21 | CE1 | PHE- 729 | 3.74 | 0 | Hydrophobic |
| C19 | CB | PHE- 729 | 3.95 | 0 | Hydrophobic |
| C2 | CD2 | PHE- 729 | 3.48 | 0 | Hydrophobic |
| C1 | CB | PHE- 729 | 3.71 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 729 | 3.45 | 0 | Aromatic Face/Face |
