sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.820 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 |
|---|---|
| A | 100 % |
| B-Factor: | 12.237 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.503 | 853.875 |
| % Hydrophobic | % Polar |
|---|---|
| 35.97 | 64.03 |
| According to VolSite | |
| HET Code: | KAI |
|---|---|
| Formula: | C10H14NO4 |
| Molecular weight: | 212.222 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.49 % |
| 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 |
|---|---|---|
| -1.19467 | 32.7176 | 44.4671 |
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 | 3.99 | 0 | Hydrophobic |
| CD2 | CE1 | TYR- 61 | 3.59 | 0 | Hydrophobic |
| CG2 | CE1 | TYR- 61 | 3.62 | 0 | Hydrophobic |
| N | O | PRO- 88 | 2.91 | 127.72 | H-Bond (Ligand Donor) |
| O | N | THR- 90 | 3.06 | 173.27 | H-Bond (Protein Donor) |
| O | NH2 | ARG- 95 | 3.47 | 129.71 | H-Bond (Protein Donor) |
| O | NH1 | ARG- 95 | 2.8 | 165.41 | H-Bond (Protein Donor) |
| OXT | NH2 | ARG- 95 | 2.88 | 141.25 | H-Bond (Protein Donor) |
| OXT | NH1 | ARG- 95 | 3.4 | 125.85 | H-Bond (Protein Donor) |
| O | CZ | ARG- 95 | 3.57 | 0 | Ionic (Protein Cationic) |
| OXT | CZ | ARG- 95 | 3.54 | 0 | Ionic (Protein Cationic) |
| CD2 | CG1 | VAL- 137 | 3.99 | 0 | Hydrophobic |
| OXT | OG | SER- 141 | 2.82 | 145.36 | H-Bond (Protein Donor) |
| OXT | N | SER- 141 | 2.96 | 146.76 | H-Bond (Protein Donor) |
| OD1 | OG1 | THR- 142 | 2.68 | 169.78 | H-Bond (Protein Donor) |
| OD2 | N | THR- 142 | 3 | 176.62 | H-Bond (Protein Donor) |
| OD2 | OG1 | THR- 142 | 3.49 | 121.53 | H-Bond (Protein Donor) |
| N | OE2 | GLU- 190 | 3.6 | 0 | Ionic (Ligand Cationic) |
| N | OE1 | GLU- 190 | 2.83 | 0 | Ionic (Ligand Cationic) |
| N | OE1 | GLU- 190 | 2.83 | 157.13 | H-Bond (Ligand Donor) |
| CB1 | CG | GLU- 190 | 4.5 | 0 | Hydrophobic |
