sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.320 Å
X-ray
2013-06-18
| Name: | Rhodopsin kinase |
|---|---|
| ID: | RK_BOVIN |
| AC: | P28327 |
| Organism: | Bos taurus |
| Reign: | Eukaryota |
| TaxID: | 9913 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 47.302 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.168 | 931.500 |
| % Hydrophobic | % Polar |
|---|---|
| 46.01 | 53.99 |
| According to VolSite | |
| HET Code: | 8PR |
|---|---|
| Formula: | C19H21FNO3 |
| Molecular weight: | 330.373 g/mol |
| DrugBank ID: | DB00715 |
| Buried Surface Area: | 57.12 % |
| Polar Surface area: | 44.3 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -29.6386 | 41.4388 | 17.7483 |
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 |
| CAG | CB | LEU- 193 | 4.02 | 0 | Hydrophobic |
| CAS | CG2 | VAL- 201 | 3.83 | 0 | Hydrophobic |
| CAC | CG2 | VAL- 201 | 3.56 | 0 | Hydrophobic |
| CAU | CG1 | VAL- 201 | 3.76 | 0 | Hydrophobic |
| CAL | CB | ALA- 214 | 3.41 | 0 | Hydrophobic |
| CAU | CB | ALA- 214 | 4.19 | 0 | Hydrophobic |
| FAA | CG | LYS- 216 | 3.98 | 0 | Hydrophobic |
| CAR | CD | LYS- 216 | 4.42 | 0 | Hydrophobic |
| FAA | CD2 | LEU- 218 | 4.15 | 0 | Hydrophobic |
| CAL | CG1 | VAL- 248 | 4.31 | 0 | Hydrophobic |
| CAL | CG | MET- 264 | 3.92 | 0 | Hydrophobic |
| CAL | CG | MET- 267 | 3.85 | 0 | Hydrophobic |
| CAU | CB | MET- 267 | 4.1 | 0 | Hydrophobic |
| OAP | N | MET- 267 | 3.34 | 149.47 | H-Bond (Protein Donor) |
| NAN | OD2 | ASP- 271 | 2.82 | 163.43 | H-Bond (Ligand Donor) |
| NAN | OD2 | ASP- 271 | 2.82 | 0 | Ionic (Ligand Cationic) |
| CAL | CD1 | LEU- 321 | 4.24 | 0 | Hydrophobic |
| CAM | CD2 | LEU- 321 | 4.32 | 0 | Hydrophobic |
| CAV | CD1 | LEU- 321 | 3.43 | 0 | Hydrophobic |
