sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 Å
X-ray
2007-11-11
| Name: | Glutamate receptor 2 |
|---|---|
| ID: | GRIA2_RAT |
| AC: | P19491 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 46 % |
| B | 54 % |
| B-Factor: | 6.162 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.784 | 722.250 |
| % Hydrophobic | % Polar |
|---|---|
| 34.11 | 65.89 |
| According to VolSite | |
| HET Code: | BHY |
|---|---|
| Formula: | C20H28N2O4S2 |
| Molecular weight: | 424.577 g/mol |
| DrugBank ID: | DB07455 |
| Buried Surface Area: | 68.65 % |
| Polar Surface area: | 109.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 79.1578 | 16.6293 | 28.7658 |
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 | CG2 | ILE- 92 | 4.44 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 92 | 3.96 | 0 | Hydrophobic |
| C19 | CG | LYS- 104 | 3.9 | 0 | Hydrophobic |
| C20 | CB | LYS- 104 | 3.34 | 0 | Hydrophobic |
| N1 | O | PRO- 105 | 2.7 | 149.24 | H-Bond (Ligand Donor) |
| N2 | O | PRO- 105 | 2.75 | 151.23 | H-Bond (Ligand Donor) |
| C6 | CB | PRO- 105 | 3.44 | 0 | Hydrophobic |
| C7 | CG | PRO- 105 | 4.37 | 0 | Hydrophobic |
| C10 | CG | PRO- 105 | 4.1 | 0 | Hydrophobic |
| C19 | CG | PRO- 105 | 4.01 | 0 | Hydrophobic |
| C20 | CG | PRO- 105 | 3.68 | 0 | Hydrophobic |
| C20 | CG | PRO- 105 | 4.22 | 0 | Hydrophobic |
| C8 | CB | PRO- 105 | 3.53 | 0 | Hydrophobic |
| C5 | CG | PRO- 105 | 3.49 | 0 | Hydrophobic |
| C3 | CB | SER- 108 | 4.46 | 0 | Hydrophobic |
| C11 | CB | SER- 108 | 4.48 | 0 | Hydrophobic |
| C5 | CB | SER- 108 | 3.64 | 0 | Hydrophobic |
| C9 | CB | SER- 108 | 3.56 | 0 | Hydrophobic |
| C16 | CB | SER- 217 | 3.82 | 0 | Hydrophobic |
| C17 | CB | SER- 217 | 3.85 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 239 | 3.62 | 0 | Hydrophobic |
| O1 | O | HOH- 416 | 2.77 | 143.45 | H-Bond (Protein Donor) |
