sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2002-10-09
| Name: | Retinoic acid receptor RXR-alpha |
|---|---|
| ID: | RXRA_HUMAN |
| AC: | P19793 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 15.722 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.753 | 479.250 |
| % Hydrophobic | % Polar |
|---|---|
| 73.24 | 26.76 |
| According to VolSite | |
| HET Code: | BM6 |
|---|---|
| Formula: | C24H27O4 |
| Molecular weight: | 379.469 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 76.41 % |
| Polar Surface area: | 58.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -7.12843 | -5.02018 | -5.32179 |
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 |
| C24 | CG1 | VAL- 265 | 4.32 | 0 | Hydrophobic |
| C21 | CG2 | ILE- 268 | 4.48 | 0 | Hydrophobic |
| C4 | CG2 | ILE- 268 | 3.73 | 0 | Hydrophobic |
| C24 | CG2 | ILE- 268 | 4.02 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 268 | 3.6 | 0 | Hydrophobic |
| C3 | CB | ALA- 271 | 4.17 | 0 | Hydrophobic |
| C8 | CB | ALA- 272 | 4.12 | 0 | Hydrophobic |
| C10 | CB | ALA- 272 | 4.43 | 0 | Hydrophobic |
| C6 | CB | ALA- 272 | 3.65 | 0 | Hydrophobic |
| C7 | CG | GLN- 275 | 4.17 | 0 | Hydrophobic |
| C19 | CZ3 | TRP- 305 | 3.74 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 309 | 4.49 | 0 | Hydrophobic |
| C20 | CB | LEU- 309 | 4.4 | 0 | Hydrophobic |
| C6 | CB | LEU- 309 | 3.58 | 0 | Hydrophobic |
| C20 | CG1 | ILE- 310 | 3.5 | 0 | Hydrophobic |
| C2 | CB | PHE- 313 | 4.28 | 0 | Hydrophobic |
| C8 | CE2 | PHE- 313 | 4.05 | 0 | Hydrophobic |
| C21 | CZ | PHE- 313 | 3.87 | 0 | Hydrophobic |
| C22 | CZ | PHE- 313 | 4.15 | 0 | Hydrophobic |
| O1 | NH2 | ARG- 316 | 3.01 | 145.22 | H-Bond (Protein Donor) |
| O1 | NH1 | ARG- 316 | 2.98 | 147.08 | H-Bond (Protein Donor) |
| O2 | NH1 | ARG- 316 | 3.23 | 152.07 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 316 | 3.43 | 0 | Ionic (Protein Cationic) |
| C21 | CD1 | ILE- 324 | 3.87 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 326 | 4 | 0 | Hydrophobic |
| O2 | N | ALA- 327 | 2.82 | 158.09 | H-Bond (Protein Donor) |
| C17 | CB | VAL- 342 | 4.12 | 0 | Hydrophobic |
| C22 | CG1 | ILE- 345 | 4.34 | 0 | Hydrophobic |
| C17 | CG2 | ILE- 345 | 3.88 | 0 | Hydrophobic |
| C21 | CD1 | PHE- 346 | 4.09 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 349 | 4.16 | 0 | Hydrophobic |
| C22 | SG | CYS- 432 | 4.08 | 0 | Hydrophobic |
| C23 | SG | CYS- 432 | 4.3 | 0 | Hydrophobic |
| C20 | SG | CYS- 432 | 3.63 | 0 | Hydrophobic |
| C14 | SG | CYS- 432 | 3.72 | 0 | Hydrophobic |
| C23 | CB | HIS- 435 | 3.45 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 436 | 4.1 | 0 | Hydrophobic |
| C23 | CG | LEU- 436 | 4.5 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 436 | 3.91 | 0 | Hydrophobic |
| C23 | CE1 | PHE- 439 | 3.82 | 0 | Hydrophobic |
| C24 | CE1 | PHE- 439 | 4.11 | 0 | Hydrophobic |
