sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2009-04-08
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.720 | 7.300 | 7.520 | 0.710 | 7.850 | 12 |
| 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: | 65.810 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 2.334 | 546.750 |
| % Hydrophobic | % Polar |
|---|---|
| 83.95 | 16.05 |
| According to VolSite | |
| HET Code: | 9RA |
|---|---|
| Formula: | C24H27O2 |
| Molecular weight: | 347.470 g/mol |
| DrugBank ID: | DB00307 |
| Buried Surface Area: | 71.45 % |
| Polar Surface area: | 40.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 0 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 62.3863 | 9.59331 | 36.5713 |
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 | CG2 | ILE- 268 | 3.61 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 268 | 3.65 | 0 | Hydrophobic |
| C21 | CG2 | ILE- 268 | 4.41 | 0 | Hydrophobic |
| C1 | CG2 | ILE- 268 | 3.65 | 0 | Hydrophobic |
| C43 | CB | ALA- 272 | 4.23 | 0 | Hydrophobic |
| C13 | CB | ALA- 272 | 3.53 | 0 | Hydrophobic |
| C12 | CG | GLN- 275 | 4.03 | 0 | Hydrophobic |
| C43 | CH2 | TRP- 305 | 3.94 | 0 | Hydrophobic |
| C12 | CG | LEU- 309 | 3.7 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 309 | 3.57 | 0 | Hydrophobic |
| C11 | CB | PHE- 313 | 4.14 | 0 | Hydrophobic |
| O53 | NH1 | ARG- 316 | 3.22 | 161.13 | H-Bond (Protein Donor) |
| C27 | CD1 | ILE- 324 | 4.49 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 326 | 3.63 | 0 | Hydrophobic |
| C20 | CB | VAL- 342 | 4.34 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 342 | 3.82 | 0 | Hydrophobic |
| C31 | CD1 | ILE- 345 | 3.43 | 0 | Hydrophobic |
| C20 | CG2 | ILE- 345 | 4.24 | 0 | Hydrophobic |
| C39 | CD1 | ILE- 345 | 4.39 | 0 | Hydrophobic |
| C27 | CE2 | PHE- 346 | 3.87 | 0 | Hydrophobic |
| C20 | CD2 | PHE- 346 | 4.49 | 0 | Hydrophobic |
| C31 | CG2 | VAL- 349 | 4.16 | 0 | Hydrophobic |
| C39 | SG | CYS- 432 | 4.2 | 0 | Hydrophobic |
| C3 | SG | CYS- 432 | 3.45 | 0 | Hydrophobic |
| C2 | SG | CYS- 432 | 3.57 | 0 | Hydrophobic |
| C39 | CB | HIS- 435 | 3.69 | 0 | Hydrophobic |
| C43 | CD1 | LEU- 436 | 3.33 | 0 | Hydrophobic |
| C35 | CD2 | LEU- 436 | 3.87 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 436 | 3.47 | 0 | Hydrophobic |
| C35 | CE2 | PHE- 439 | 3.9 | 0 | Hydrophobic |
