sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2007-03-29
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.540 | 5.540 | 5.540 | 0.000 | 5.540 | 1 |
| 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: | 18.312 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.718 | 850.500 |
| % Hydrophobic | % Polar |
|---|---|
| 38.49 | 61.51 |
| According to VolSite | |
| HET Code: | AT1 |
|---|---|
| Formula: | C11H17N2O7P |
| Molecular weight: | 320.236 g/mol |
| DrugBank ID: | DB02347 |
| Buried Surface Area: | 57.05 % |
| Polar Surface area: | 176.03 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 3 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 39.0836 | 5.01962 | 6.71971 |
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 |
| C9 | CG | GLU- 13 | 3.77 | 0 | Hydrophobic |
| C11 | CG | GLU- 13 | 4.25 | 0 | Hydrophobic |
| C10 | CE2 | TYR- 16 | 4.4 | 0 | Hydrophobic |
| C11 | CE2 | TYR- 16 | 4.39 | 0 | Hydrophobic |
| C | CE2 | TYR- 61 | 4.05 | 0 | Hydrophobic |
| C11 | CZ | TYR- 61 | 3.83 | 0 | Hydrophobic |
| N | O | PRO- 88 | 2.92 | 169.43 | H-Bond (Ligand Donor) |
| C11 | CG | PRO- 88 | 3.27 | 0 | Hydrophobic |
| N | OG1 | THR- 90 | 2.66 | 167.39 | H-Bond (Ligand Donor) |
| O | N | THR- 90 | 2.71 | 172.1 | H-Bond (Protein Donor) |
| O | CZ | ARG- 95 | 3.61 | 0 | Ionic (Protein Cationic) |
| O1 | CZ | ARG- 95 | 3.66 | 0 | Ionic (Protein Cationic) |
| O | NH1 | ARG- 95 | 2.79 | 154.91 | H-Bond (Protein Donor) |
| O1 | NH2 | ARG- 95 | 2.85 | 175.93 | H-Bond (Protein Donor) |
| O4 | OG | SER- 141 | 2.74 | 156.33 | H-Bond (Protein Donor) |
| O5 | N | SER- 141 | 2.71 | 159.48 | H-Bond (Protein Donor) |
| N | OE1 | GLU- 190 | 3.95 | 0 | Ionic (Ligand Cationic) |
| N | OE2 | GLU- 190 | 2.91 | 0 | Ionic (Ligand Cationic) |
| N | OE2 | GLU- 190 | 2.91 | 163.79 | H-Bond (Ligand Donor) |
| C10 | CG | GLU- 190 | 4.13 | 0 | Hydrophobic |
| C10 | CZ | TYR- 216 | 4.26 | 0 | Hydrophobic |
