sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.550 Å
X-ray
2012-10-05
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.910 | 4.910 | 4.910 | 0.000 | 4.920 | 3 |
| Name: | Glutamate receptor ionotropic, kainate 2 |
|---|---|
| ID: | GRIK2_RAT |
| AC: | P42260 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 42.339 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.494 | 384.750 |
| % Hydrophobic | % Polar |
|---|---|
| 49.12 | 50.88 |
| According to VolSite | |
| HET Code: | KAI |
|---|---|
| Formula: | C10H14NO4 |
| Molecular weight: | 212.222 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 72 % |
| 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 |
|---|---|---|
| 75.3587 | -1.55547 | 25.5045 |
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- 440 | 3.97 | 0 | Hydrophobic |
| CD1 | CZ | TYR- 488 | 3.31 | 0 | Hydrophobic |
| CG | CE2 | TYR- 488 | 3.51 | 0 | Hydrophobic |
| CD2 | CE1 | TYR- 488 | 3.25 | 0 | Hydrophobic |
| N | O | PRO- 516 | 2.89 | 129.82 | H-Bond (Ligand Donor) |
| O | N | ALA- 518 | 2.77 | 171.11 | H-Bond (Protein Donor) |
| O | NH1 | ARG- 523 | 2.91 | 170.09 | H-Bond (Protein Donor) |
| OXT | NH1 | ARG- 523 | 3.22 | 132.43 | H-Bond (Protein Donor) |
| OXT | NH2 | ARG- 523 | 2.9 | 145.29 | H-Bond (Protein Donor) |
| O | CZ | ARG- 523 | 3.79 | 0 | Ionic (Protein Cationic) |
| OXT | CZ | ARG- 523 | 3.47 | 0 | Ionic (Protein Cationic) |
| CD2 | CG1 | VAL- 685 | 4.2 | 0 | Hydrophobic |
| OXT | N | ALA- 689 | 3.1 | 137.3 | H-Bond (Protein Donor) |
| OD1 | OG1 | THR- 690 | 2.86 | 176.7 | H-Bond (Protein Donor) |
| OD2 | N | THR- 690 | 3.09 | 160.68 | H-Bond (Protein Donor) |
| OD2 | OG1 | THR- 690 | 3.21 | 120.6 | H-Bond (Protein Donor) |
| N | OE1 | GLU- 738 | 2.76 | 155.75 | H-Bond (Ligand Donor) |
| N | OE1 | GLU- 738 | 2.76 | 0 | Ionic (Ligand Cationic) |
| N | OE2 | GLU- 738 | 3.03 | 0 | Ionic (Ligand Cationic) |
