sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2012-02-16
| 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 | 3 % |
| D | 97 % |
| B-Factor: | 54.802 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.090 | 695.250 |
| % Hydrophobic | % Polar |
|---|---|
| 57.28 | 42.72 |
| According to VolSite | |
| HET Code: | 3A6 |
|---|---|
| Formula: | C23H19FN4O3S |
| Molecular weight: | 450.485 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 55.62 % |
| Polar Surface area: | 123.41 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 23.0033 | 35.3725 | 22.5922 |
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 |
| C1 | CE2 | TYR- 524 | 4.35 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 675 | 4.18 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 678 | 4.49 | 0 | Hydrophobic |
| C31 | CD | LYS- 686 | 4.17 | 0 | Hydrophobic |
| C1 | CD1 | ILE- 692 | 4.14 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 692 | 4.16 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 692 | 4.18 | 0 | Hydrophobic |
| N23 | OH | TYR- 693 | 2.76 | 169.49 | H-Bond (Protein Donor) |
| C13 | CE2 | PHE- 696 | 3.48 | 0 | Hydrophobic |
| F24 | CB | PRO- 712 | 3.44 | 0 | Hydrophobic |
| C11 | CB | MET- 713 | 4.36 | 0 | Hydrophobic |
| C12 | SD | MET- 713 | 3.99 | 0 | Hydrophobic |
| C21 | CB | MET- 713 | 4.47 | 0 | Hydrophobic |
| C17 | CB | MET- 713 | 3.58 | 0 | Hydrophobic |
| F24 | CB | LYS- 718 | 3.57 | 0 | Hydrophobic |
| F24 | CG | GLU- 721 | 4.15 | 0 | Hydrophobic |
| C19 | CB | GLU- 721 | 3.89 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 722 | 3.61 | 0 | Hydrophobic |
| C9 | CB | PHE- 729 | 3.4 | 0 | Hydrophobic |
