sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2009-04-24
| 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 | 33 % |
| B | 67 % |
| B-Factor: | 14.518 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.280 | 816.750 |
| % Hydrophobic | % Polar |
|---|---|
| 37.60 | 62.40 |
| According to VolSite | |
| HET Code: | NS6 |
|---|---|
| Formula: | C18H28N3O4S2 |
| Molecular weight: | 414.563 g/mol |
| DrugBank ID: | DB08304 |
| Buried Surface Area: | 53.91 % |
| Polar Surface area: | 104.75 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 73.4125 | 20.6578 | 45.8527 |
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 |
| C3 | CB | ILE- 92 | 4.19 | 0 | Hydrophobic |
| C4 | CG2 | ILE- 92 | 3.78 | 0 | Hydrophobic |
| C4 | CG | LYS- 104 | 4.27 | 0 | Hydrophobic |
| C5 | CG | PRO- 105 | 4.36 | 0 | Hydrophobic |
| C10 | CB | SER- 108 | 4.44 | 0 | Hydrophobic |
| O3 | N | SER- 108 | 3.49 | 165.29 | H-Bond (Protein Donor) |
| C14 | CB | SER- 217 | 4.25 | 0 | Hydrophobic |
| C10 | CB | SER- 217 | 4.04 | 0 | Hydrophobic |
| C3 | CB | LYS- 218 | 3.66 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 239 | 3.94 | 0 | Hydrophobic |
| C2 | CB | SER- 242 | 4.06 | 0 | Hydrophobic |
| C9 | CB | SER- 242 | 3.96 | 0 | Hydrophobic |
| C12 | CB | LEU- 247 | 3.95 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 247 | 3.75 | 0 | Hydrophobic |
| C17 | CG | LYS- 251 | 4.25 | 0 | Hydrophobic |
| O3 | O | HOH- 423 | 2.94 | 161.78 | H-Bond (Protein Donor) |
