sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.290 Å
X-ray
2012-05-08
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.700 | 5.700 | 5.700 | 0.000 | 5.700 | 1 |
| Name: | Glutamate receptor 3 |
|---|---|
| ID: | GRIA3_RAT |
| AC: | P19492 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 100 % |
| B-Factor: | 33.774 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.258 | 418.500 |
| % Hydrophobic | % Polar |
|---|---|
| 35.48 | 64.52 |
| According to VolSite | |
| HET Code: | KAI |
|---|---|
| Formula: | C10H14NO4 |
| Molecular weight: | 212.222 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 74.13 % |
| Polar Surface area: | 96.87 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -1.21053 | 17.7603 | 17.7203 |
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 |
| CD2 | CE1 | TYR- 61 | 3.37 | 0 | Hydrophobic |
| CG | CE1 | TYR- 61 | 3.66 | 0 | Hydrophobic |
| N | O | PRO- 89 | 2.8 | 134.55 | H-Bond (Ligand Donor) |
| O | N | THR- 91 | 2.8 | 174.18 | H-Bond (Protein Donor) |
| O | NH1 | ARG- 96 | 2.89 | 149.56 | H-Bond (Protein Donor) |
| OXT | NH1 | ARG- 96 | 3.3 | 134.42 | H-Bond (Protein Donor) |
| OXT | NH2 | ARG- 96 | 2.98 | 147.69 | H-Bond (Protein Donor) |
| O | CZ | ARG- 96 | 3.63 | 0 | Ionic (Protein Cationic) |
| OXT | CZ | ARG- 96 | 3.56 | 0 | Ionic (Protein Cationic) |
| CD2 | CD2 | LEU- 138 | 4.09 | 0 | Hydrophobic |
| CB1 | CD2 | LEU- 138 | 4.18 | 0 | Hydrophobic |
| OXT | N | SER- 142 | 3.08 | 160.33 | H-Bond (Protein Donor) |
| OD2 | OG1 | THR- 143 | 3.1 | 120.07 | H-Bond (Protein Donor) |
| OD2 | N | THR- 143 | 2.87 | 169.99 | H-Bond (Protein Donor) |
| N | OE1 | GLU- 193 | 2.81 | 145.93 | H-Bond (Ligand Donor) |
| N | OE1 | GLU- 193 | 2.81 | 0 | Ionic (Ligand Cationic) |
| N | OE2 | GLU- 193 | 3.63 | 0 | Ionic (Ligand Cationic) |
| CB1 | CG | GLU- 193 | 4.46 | 0 | Hydrophobic |
| OD1 | O | HOH- 471 | 2.81 | 143.6 | H-Bond (Protein Donor) |
