sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.970 Å
X-ray
2008-01-27
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.090 | 5.090 | 5.090 | 0.000 | 5.090 | 3 |
| Name: | Glutamate receptor ionotropic, kainate 1 |
|---|---|
| ID: | GRIK1_RAT |
| AC: | P22756 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 15.638 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.748 | 745.875 |
| % Hydrophobic | % Polar |
|---|---|
| 43.89 | 56.11 |
| According to VolSite | |
| HET Code: | KAI |
|---|---|
| Formula: | C10H14NO4 |
| Molecular weight: | 212.222 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.46 % |
| 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 |
|---|---|---|
| 3.201 | 35.1929 | 77.1562 |
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 |
| CD1 | CG | GLU- 13 | 4.11 | 0 | Hydrophobic |
| CG | CZ | TYR- 61 | 3.63 | 0 | Hydrophobic |
| CD2 | CE2 | TYR- 61 | 3.38 | 0 | Hydrophobic |
| N | O | PRO- 88 | 2.87 | 133.12 | H-Bond (Ligand Donor) |
| O | N | THR- 90 | 3.11 | 175.59 | H-Bond (Protein Donor) |
| O | CZ | ARG- 95 | 3.57 | 0 | Ionic (Protein Cationic) |
| OXT | CZ | ARG- 95 | 3.57 | 0 | Ionic (Protein Cationic) |
| O | NH1 | ARG- 95 | 2.86 | 160.07 | H-Bond (Protein Donor) |
| O | NH2 | ARG- 95 | 3.41 | 132.37 | H-Bond (Protein Donor) |
| OXT | NH1 | ARG- 95 | 3.41 | 126.99 | H-Bond (Protein Donor) |
| OXT | NH2 | ARG- 95 | 2.94 | 141.42 | H-Bond (Protein Donor) |
| CD2 | CG1 | VAL- 137 | 3.98 | 0 | Hydrophobic |
| OXT | OG | SER- 141 | 2.69 | 150.63 | H-Bond (Protein Donor) |
| OXT | N | SER- 141 | 2.97 | 148.44 | H-Bond (Protein Donor) |
| OD1 | OG1 | THR- 142 | 2.64 | 169.8 | H-Bond (Protein Donor) |
| OD2 | N | THR- 142 | 3.08 | 172.95 | H-Bond (Protein Donor) |
| OD2 | OG1 | THR- 142 | 3.5 | 121.6 | H-Bond (Protein Donor) |
| N | OE1 | GLU- 190 | 2.87 | 158.05 | H-Bond (Ligand Donor) |
| N | OE1 | GLU- 190 | 2.87 | 0 | Ionic (Ligand Cationic) |
| N | OE2 | GLU- 190 | 3.56 | 0 | Ionic (Ligand Cationic) |
