sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2003-11-06
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.700 | 7.570 | 7.640 | 0.700 | 8.300 | 4 |
| 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: | 37.302 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.962 | 560.250 |
| % Hydrophobic | % Polar |
|---|---|
| 75.30 | 24.70 |
| According to VolSite | |
| HET Code: | L79 |
|---|---|
| Formula: | C25H29O3 |
| Molecular weight: | 377.496 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 74.23 % |
| Polar Surface area: | 49.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 9.07957 | 36.4771 | 43.8011 |
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 |
| C17 | CG1 | VAL- 265 | 4.06 | 0 | Hydrophobic |
| C17 | CG2 | ILE- 268 | 4.19 | 0 | Hydrophobic |
| C21 | CD1 | ILE- 268 | 3.89 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 268 | 3.63 | 0 | Hydrophobic |
| C8 | CB | ALA- 272 | 4.4 | 0 | Hydrophobic |
| C11 | CB | ALA- 272 | 4.34 | 0 | Hydrophobic |
| C11 | CZ3 | TRP- 305 | 3.78 | 0 | Hydrophobic |
| C11 | CB | LEU- 309 | 3.69 | 0 | Hydrophobic |
| C10 | CG1 | ILE- 310 | 4.09 | 0 | Hydrophobic |
| O1 | NH2 | ARG- 316 | 3.25 | 139.59 | H-Bond (Protein Donor) |
| O1 | NH1 | ARG- 316 | 2.99 | 153.79 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 316 | 3.56 | 0 | Ionic (Protein Cationic) |
| C21 | CD1 | ILE- 324 | 4.49 | 0 | Hydrophobic |
| O7 | N | ALA- 327 | 2.51 | 174.61 | H-Bond (Protein Donor) |
| C16 | CG1 | VAL- 342 | 3.88 | 0 | Hydrophobic |
| C22 | CB | VAL- 342 | 3.76 | 0 | Hydrophobic |
| C22 | CG2 | ILE- 345 | 3.68 | 0 | Hydrophobic |
| C21 | CD2 | PHE- 346 | 3.58 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 349 | 3.89 | 0 | Hydrophobic |
| C23 | SG | CYS- 432 | 4.14 | 0 | Hydrophobic |
| C24 | SG | CYS- 432 | 4.22 | 0 | Hydrophobic |
| C18 | CB | HIS- 435 | 3.57 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 436 | 3.67 | 0 | Hydrophobic |
| C17 | CE2 | PHE- 439 | 4.46 | 0 | Hydrophobic |
| C18 | CE2 | PHE- 439 | 4.19 | 0 | Hydrophobic |
