sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2005-07-19
| 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 |
|---|---|
| A | 6 % |
| E | 94 % |
| B-Factor: | 31.451 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 2.024 | 513.000 |
| % Hydrophobic | % Polar |
|---|---|
| 73.68 | 26.32 |
| According to VolSite | |
| HET Code: | REA |
|---|---|
| Formula: | C20H27O2 |
| Molecular weight: | 299.427 g/mol |
| DrugBank ID: | DB00755 |
| Buried Surface Area: | 63.28 % |
| 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 |
|---|---|---|
| 69.3764 | 59.569 | 96.6205 |
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 | 4.29 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 268 | 4 | 0 | Hydrophobic |
| C20 | CG2 | ILE- 268 | 4.28 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 268 | 4.16 | 0 | Hydrophobic |
| C16 | SG | CYS- 269 | 4.02 | 0 | Hydrophobic |
| C20 | CB | ALA- 271 | 3.9 | 0 | Hydrophobic |
| C19 | CZ3 | TRP- 305 | 4.13 | 0 | Hydrophobic |
| C19 | CB | ASN- 306 | 3.9 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 310 | 4.46 | 0 | Hydrophobic |
| C18 | CZ | PHE- 313 | 3.89 | 0 | Hydrophobic |
| C20 | CD2 | PHE- 313 | 3.5 | 0 | Hydrophobic |
| O1 | NH2 | ARG- 316 | 2.59 | 151.28 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 316 | 3.68 | 0 | Ionic (Protein Cationic) |
| C20 | CG | LEU- 326 | 4.18 | 0 | Hydrophobic |
| O2 | N | ALA- 327 | 2.88 | 148.02 | H-Bond (Protein Donor) |
| C3 | CG1 | VAL- 342 | 4.19 | 0 | Hydrophobic |
| C4 | CG2 | ILE- 345 | 3.86 | 0 | Hydrophobic |
| C17 | CB | CYS- 432 | 3.95 | 0 | Hydrophobic |
| C18 | SG | CYS- 432 | 4.45 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 436 | 4.13 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 436 | 4.15 | 0 | Hydrophobic |
