sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
1999-12-07
| Name: | Retinoic acid receptor alpha |
|---|---|
| ID: | RARA_HUMAN |
| AC: | P10276 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 41.874 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 45 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.685 | 685.125 |
| % Hydrophobic | % Polar |
|---|---|
| 65.02 | 34.98 |
| According to VolSite | |
| HET Code: | BMS |
|---|---|
| Formula: | C29H25N2O3 |
| Molecular weight: | 449.520 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.74 % |
| Polar Surface area: | 82.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -20.6057 | 84.292 | 0.793412 |
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 |
| C17 | CE2 | PHE- 228 | 4.39 | 0 | Hydrophobic |
| C10 | CZ | PHE- 228 | 3.34 | 0 | Hydrophobic |
| C29 | CB | SER- 229 | 3.77 | 0 | Hydrophobic |
| C3 | CB | LEU- 231 | 3.81 | 0 | Hydrophobic |
| C4 | CB | SER- 232 | 3.82 | 0 | Hydrophobic |
| C24 | CB | SER- 232 | 3.56 | 0 | Hydrophobic |
| C26 | CB | SER- 232 | 4.25 | 0 | Hydrophobic |
| C24 | CB | SER- 232 | 3.56 | 0 | Hydrophobic |
| C27 | CB | THR- 233 | 4.33 | 0 | Hydrophobic |
| C7 | SG | CYS- 235 | 3.46 | 0 | Hydrophobic |
| C2 | CB | CYS- 235 | 3.79 | 0 | Hydrophobic |
| C26 | CD1 | ILE- 236 | 3.38 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 266 | 4.06 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 266 | 4.07 | 0 | Hydrophobic |
| C6 | CG | LEU- 269 | 3.73 | 0 | Hydrophobic |
| C9 | CB | LEU- 269 | 4.34 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 270 | 3.94 | 0 | Hydrophobic |
| C6 | CB | ILE- 273 | 3.9 | 0 | Hydrophobic |
| O2 | NH1 | ARG- 276 | 3.14 | 156.71 | H-Bond (Protein Donor) |
| C3 | CD2 | PHE- 286 | 3.35 | 0 | Hydrophobic |
| O1 | N | SER- 287 | 2.94 | 163.5 | H-Bond (Protein Donor) |
| O2 | OG | SER- 287 | 2.76 | 158.04 | H-Bond (Protein Donor) |
| O2 | N | SER- 287 | 3.13 | 121.69 | H-Bond (Protein Donor) |
| C20 | CD1 | PHE- 302 | 4 | 0 | Hydrophobic |
| C13 | CE1 | PHE- 302 | 3.46 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 305 | 3.99 | 0 | Hydrophobic |
| C17 | CG | ARG- 394 | 4.42 | 0 | Hydrophobic |
| C20 | CD | ARG- 394 | 4.45 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 395 | 4.24 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 395 | 4.47 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 398 | 3.92 | 0 | Hydrophobic |
| C25 | SD | MET- 406 | 4.21 | 0 | Hydrophobic |
| C27 | CG | MET- 406 | 4 | 0 | Hydrophobic |
| C29 | CG | MET- 406 | 3.43 | 0 | Hydrophobic |
