sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2013-01-17
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 18.154 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 0.330 | 641.250 |
| % Hydrophobic | % Polar |
|---|---|
| 40.53 | 59.47 |
| According to VolSite | |
| HET Code: | IKM |
|---|---|
| Formula: | C12H13N2O6 |
| Molecular weight: | 281.241 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.59 % |
| Polar Surface area: | 135.19 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -23.6488 | 62.0408 | 49.9375 |
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 |
| C5 | CE2 | TYR- 61 | 3.8 | 0 | Hydrophobic |
| N2 | O | PRO- 89 | 3.12 | 141.83 | H-Bond (Ligand Donor) |
| O6 | N | THR- 91 | 2.93 | 163.96 | H-Bond (Protein Donor) |
| O6 | OG1 | THR- 91 | 2.89 | 148.26 | H-Bond (Protein Donor) |
| O3 | NH2 | ARG- 96 | 2.72 | 134.46 | H-Bond (Protein Donor) |
| O6 | NH1 | ARG- 96 | 2.96 | 141.56 | H-Bond (Protein Donor) |
| O3 | CZ | ARG- 96 | 3.59 | 0 | Ionic (Protein Cationic) |
| O6 | CZ | ARG- 96 | 3.65 | 0 | Ionic (Protein Cationic) |
| O4 | N | SER- 142 | 2.66 | 141.83 | H-Bond (Protein Donor) |
| C8 | CG | GLU- 193 | 4.34 | 0 | Hydrophobic |
| N1 | OE1 | GLU- 193 | 3 | 161.89 | H-Bond (Ligand Donor) |
| N1 | OE2 | GLU- 193 | 2.72 | 131.6 | H-Bond (Ligand Donor) |
| N1 | OE1 | GLU- 193 | 3 | 0 | Ionic (Ligand Cationic) |
| N1 | OE2 | GLU- 193 | 2.72 | 0 | Ionic (Ligand Cationic) |
