sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2013-04-12
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.730 | 6.640 | 6.680 | 0.840 | 7.480 | 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: | 30.542 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.981 | 378.000 |
| % Hydrophobic | % Polar |
|---|---|
| 83.93 | 16.07 |
| According to VolSite | |
| HET Code: | 1O8 |
|---|---|
| Formula: | C20H21O2 |
| Molecular weight: | 293.380 g/mol |
| DrugBank ID: | DB12316 |
| Buried Surface Area: | 70.5 % |
| Polar Surface area: | 40.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 0 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 62.8546 | 47.1226 | 30.5955 |
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 |
| C2' | CG2 | ILE- 268 | 3.94 | 0 | Hydrophobic |
| C20 | CG2 | ILE- 268 | 4.07 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 268 | 4.25 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 268 | 3.83 | 0 | Hydrophobic |
| C20 | CB | ALA- 271 | 3.89 | 0 | Hydrophobic |
| C19 | CZ3 | TRP- 305 | 4.02 | 0 | Hydrophobic |
| C19 | CB | ASN- 306 | 4.34 | 0 | Hydrophobic |
| C20 | CD2 | PHE- 313 | 3.76 | 0 | Hydrophobic |
| O1 | NH2 | ARG- 316 | 3 | 138.56 | H-Bond (Protein Donor) |
| O1 | NH1 | ARG- 316 | 2.86 | 145.24 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 316 | 3.35 | 0 | Ionic (Protein Cationic) |
| C20 | CD2 | LEU- 326 | 3.88 | 0 | Hydrophobic |
| O2 | N | ALA- 327 | 2.96 | 169.63 | H-Bond (Protein Donor) |
| C4 | CB | VAL- 342 | 4.32 | 0 | Hydrophobic |
| C4 | CG2 | ILE- 345 | 3.77 | 0 | Hydrophobic |
| C19 | CB | CYS- 432 | 4.08 | 0 | Hydrophobic |
| C1' | CB | CYS- 432 | 4.34 | 0 | Hydrophobic |
| C6 | SG | CYS- 432 | 3.65 | 0 | Hydrophobic |
| C1 | SG | CYS- 432 | 3.73 | 0 | Hydrophobic |
| C1' | CB | HIS- 435 | 4.21 | 0 | Hydrophobic |
| C2' | CD2 | LEU- 436 | 3.67 | 0 | Hydrophobic |
| C1' | CG | LEU- 436 | 3.65 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 436 | 3.4 | 0 | Hydrophobic |
| C18 | CE1 | PHE- 439 | 3.93 | 0 | Hydrophobic |
