sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2001-10-18
| 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 | 100 % |
| B-Factor: | 41.293 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 2.093 | 455.625 |
| % Hydrophobic | % Polar |
|---|---|
| 82.96 | 17.04 |
| According to VolSite | |
| HET Code: | 9CR |
|---|---|
| Formula: | C20H27O2 |
| Molecular weight: | 299.427 g/mol |
| DrugBank ID: | DB00523 |
| Buried Surface Area: | 66.08 % |
| 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 |
|---|---|---|
| 13.8602 | 16.9686 | 44.7955 |
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 |
| C18 | CD1 | ILE- 268 | 3.71 | 0 | Hydrophobic |
| C20 | CG2 | ILE- 268 | 4.21 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 268 | 3.75 | 0 | Hydrophobic |
| C20 | CB | ALA- 271 | 4.27 | 0 | Hydrophobic |
| C19 | CZ3 | TRP- 305 | 3.64 | 0 | Hydrophobic |
| C19 | CB | ASN- 306 | 4.48 | 0 | Hydrophobic |
| C18 | CZ | PHE- 313 | 4.14 | 0 | Hydrophobic |
| C20 | CD2 | PHE- 313 | 3.37 | 0 | Hydrophobic |
| O1 | NH2 | ARG- 316 | 2.83 | 154.48 | H-Bond (Protein Donor) |
| O1 | NH1 | ARG- 316 | 3.2 | 135.43 | H-Bond (Protein Donor) |
| O2 | NH1 | ARG- 316 | 3.34 | 145.61 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 316 | 3.45 | 0 | Ionic (Protein Cationic) |
| C20 | CD2 | LEU- 326 | 3.61 | 0 | Hydrophobic |
| O2 | N | ALA- 327 | 2.64 | 141.66 | H-Bond (Protein Donor) |
| C2 | CG1 | VAL- 342 | 4.22 | 0 | Hydrophobic |
| C3 | CB | VAL- 342 | 3.79 | 0 | Hydrophobic |
| C2 | CG2 | ILE- 345 | 3.88 | 0 | Hydrophobic |
| C1 | SG | CYS- 432 | 4.33 | 0 | Hydrophobic |
| C17 | CB | CYS- 432 | 3.31 | 0 | Hydrophobic |
| C17 | CB | HIS- 435 | 3.65 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 436 | 3.93 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 436 | 3.69 | 0 | Hydrophobic |
| C16 | CE2 | PHE- 439 | 3.85 | 0 | Hydrophobic |
