sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.360 Å
X-ray
2008-11-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.740 | 7.630 | 7.970 | 0.900 | 8.820 | 14 |
| 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 |
|---|---|
| C | 100 % |
| B-Factor: | 30.435 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.500 | 786.375 |
| % Hydrophobic | % Polar |
|---|---|
| 58.80 | 41.20 |
| According to VolSite | |
| HET Code: | REA |
|---|---|
| Formula: | C20H27O2 |
| Molecular weight: | 299.427 g/mol |
| DrugBank ID: | DB00755 |
| Buried Surface Area: | 60.09 % |
| Polar Surface area: | 40.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 82.3655 | 58.6111 | 10.2386 |
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 |
| C16 | CG1 | VAL- 265 | 4.31 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 268 | 3.91 | 0 | Hydrophobic |
| C20 | CG2 | ILE- 268 | 3.82 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 268 | 4.13 | 0 | Hydrophobic |
| C16 | SG | CYS- 269 | 4.21 | 0 | Hydrophobic |
| C20 | CB | ALA- 271 | 3.89 | 0 | Hydrophobic |
| C19 | CB | ASN- 306 | 4.3 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 310 | 4.33 | 0 | Hydrophobic |
| C18 | CZ | PHE- 313 | 3.91 | 0 | Hydrophobic |
| C20 | CD2 | PHE- 313 | 3.53 | 0 | Hydrophobic |
| O1 | NH2 | ARG- 316 | 2.81 | 144.15 | H-Bond (Protein Donor) |
| O1 | NH1 | ARG- 316 | 2.94 | 137.69 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 316 | 3.29 | 0 | Ionic (Protein Cationic) |
| C20 | CD2 | LEU- 326 | 4.01 | 0 | Hydrophobic |
| O2 | N | ALA- 327 | 2.92 | 156.69 | H-Bond (Protein Donor) |
| C2 | CG1 | VAL- 342 | 4.23 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 342 | 4.07 | 0 | Hydrophobic |
| C4 | CG2 | ILE- 345 | 3.89 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 349 | 4.49 | 0 | Hydrophobic |
| C17 | CB | CYS- 432 | 4.3 | 0 | Hydrophobic |
| C18 | SG | CYS- 432 | 3.72 | 0 | Hydrophobic |
| C19 | CB | CYS- 432 | 4.21 | 0 | Hydrophobic |
