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
2012-10-04
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 36.639 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | ZN ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.090 | 705.375 |
| % Hydrophobic | % Polar |
|---|---|
| 59.33 | 40.67 |
| According to VolSite | |
| HET Code: | 15H |
|---|---|
| Formula: | C24H25N5O2S |
| Molecular weight: | 447.553 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.24 % |
| Polar Surface area: | 111.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 14.0721 | 89.0418 | 40.8215 |
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 | CE2 | TYR- 514 | 3.69 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 625 | 4.28 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 665 | 3.69 | 0 | Hydrophobic |
| C18 | CG2 | ILE- 682 | 4.17 | 0 | Hydrophobic |
| N4 | OH | TYR- 683 | 2.99 | 164.45 | H-Bond (Protein Donor) |
| C21 | CZ | PHE- 686 | 4.39 | 0 | Hydrophobic |
| C19 | CZ | PHE- 686 | 4.44 | 0 | Hydrophobic |
| C24 | CZ | PHE- 686 | 4.33 | 0 | Hydrophobic |
| C6 | CE2 | PHE- 686 | 3.43 | 0 | Hydrophobic |
| C14 | CB | PRO- 702 | 3.6 | 0 | Hydrophobic |
| S1 | CB | MET- 703 | 3.89 | 0 | Hydrophobic |
| C7 | CG | MET- 703 | 3.56 | 0 | Hydrophobic |
| C8 | SD | MET- 703 | 3.59 | 0 | Hydrophobic |
| C15 | CB | GLU- 711 | 3.55 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 712 | 3.83 | 0 | Hydrophobic |
| N2 | NE2 | GLN- 716 | 3.14 | 169.8 | H-Bond (Protein Donor) |
| C22 | CZ | PHE- 719 | 3.81 | 0 | Hydrophobic |
| C10 | CD1 | PHE- 719 | 3.41 | 0 | Hydrophobic |
| C9 | CB | PHE- 719 | 3.64 | 0 | Hydrophobic |
