sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.060 Å
X-ray
2012-05-09
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 25.941 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.574 | 462.375 |
| % Hydrophobic | % Polar |
|---|---|
| 42.34 | 57.66 |
| According to VolSite | |
| HET Code: | KAI |
|---|---|
| Formula: | C10H14NO4 |
| Molecular weight: | 212.222 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 72.24 % |
| 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 |
|---|---|---|
| 4.25927 | 1.55207 | 18.3275 |
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 | 3.49 | 0 | Hydrophobic |
| CG | CE1 | TYR- 61 | 3.54 | 0 | Hydrophobic |
| N | O | PRO- 89 | 3.07 | 131.99 | H-Bond (Ligand Donor) |
| O | N | THR- 91 | 2.97 | 171.27 | H-Bond (Protein Donor) |
| O | NH2 | ARG- 96 | 3.44 | 127.5 | H-Bond (Protein Donor) |
| O | NH1 | ARG- 96 | 2.79 | 152.3 | H-Bond (Protein Donor) |
| OXT | NH2 | ARG- 96 | 2.88 | 152.21 | H-Bond (Protein Donor) |
| OXT | NH1 | ARG- 96 | 3.39 | 130.94 | H-Bond (Protein Donor) |
| O | CZ | ARG- 96 | 3.54 | 0 | Ionic (Protein Cationic) |
| OXT | CZ | ARG- 96 | 3.57 | 0 | Ionic (Protein Cationic) |
| CD2 | CD1 | LEU- 138 | 3.71 | 0 | Hydrophobic |
| CB1 | CD1 | LEU- 138 | 3.92 | 0 | Hydrophobic |
| OXT | N | SER- 142 | 2.92 | 145.9 | H-Bond (Protein Donor) |
| OD1 | OG1 | THR- 143 | 2.57 | 174.18 | H-Bond (Protein Donor) |
| OD2 | N | THR- 143 | 3.01 | 175.06 | H-Bond (Protein Donor) |
| N | OE1 | GLU- 193 | 2.72 | 177.08 | H-Bond (Ligand Donor) |
| N | OE1 | GLU- 193 | 2.72 | 0 | Ionic (Ligand Cationic) |
| N | OE2 | GLU- 193 | 3.51 | 0 | Ionic (Ligand Cationic) |
| OD1 | O | HOH- 409 | 2.91 | 131.8 | H-Bond (Protein Donor) |
