sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2009-10-27
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.450 | 5.450 | 5.450 | 0.000 | 5.450 | 1 |
| Name: | Glutamate receptor 4 |
|---|---|
| ID: | GRIA4_RAT |
| AC: | P19493 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 11.753 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.860 | 918.000 |
| % Hydrophobic | % Polar |
|---|---|
| 44.12 | 55.88 |
| According to VolSite | |
| HET Code: | KAI |
|---|---|
| Formula: | C10H14NO4 |
| Molecular weight: | 212.222 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.34 % |
| 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 |
|---|---|---|
| -33.8291 | 48.2051 | -46.099 |
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- 57 | 3.82 | 0 | Hydrophobic |
| CG | CE1 | TYR- 57 | 3.69 | 0 | Hydrophobic |
| N | O | PRO- 85 | 2.96 | 124.86 | H-Bond (Ligand Donor) |
| OXT | N | THR- 87 | 3.11 | 170.18 | H-Bond (Protein Donor) |
| O | CZ | ARG- 92 | 3.71 | 0 | Ionic (Protein Cationic) |
| OXT | CZ | ARG- 92 | 3.42 | 0 | Ionic (Protein Cationic) |
| O | NH2 | ARG- 92 | 3.01 | 147.69 | H-Bond (Protein Donor) |
| OXT | NH2 | ARG- 92 | 3.25 | 132.24 | H-Bond (Protein Donor) |
| OXT | NH1 | ARG- 92 | 2.75 | 159.89 | H-Bond (Protein Donor) |
| CD2 | CG1 | VAL- 134 | 3.7 | 0 | Hydrophobic |
| CB1 | CG1 | VAL- 134 | 3.96 | 0 | Hydrophobic |
| O | N | SER- 138 | 3.01 | 149.84 | H-Bond (Protein Donor) |
| OD1 | OG1 | THR- 139 | 2.5 | 168.18 | H-Bond (Protein Donor) |
| OD2 | OG1 | THR- 139 | 3.41 | 123.07 | H-Bond (Protein Donor) |
| OD2 | N | THR- 139 | 3.11 | 168.33 | H-Bond (Protein Donor) |
| N | OE1 | GLU- 189 | 3.1 | 165.58 | H-Bond (Ligand Donor) |
| N | OE1 | GLU- 189 | 3.1 | 0 | Ionic (Ligand Cationic) |
| N | OE2 | GLU- 189 | 3.49 | 0 | Ionic (Ligand Cationic) |
| CB1 | CG | GLU- 189 | 4.39 | 0 | Hydrophobic |
| OD2 | O | HOH- 298 | 2.85 | 179.98 | H-Bond (Protein Donor) |
