sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2013-08-13
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.600 | 7.600 | 7.600 | 0.000 | 7.600 | 2 |
| 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: | 23.893 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.941 | 469.125 |
| % Hydrophobic | % Polar |
|---|---|
| 79.86 | 20.14 |
| According to VolSite | |
| HET Code: | R4M |
|---|---|
| Formula: | C21H25O2 |
| Molecular weight: | 309.422 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.23 % |
| 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: | 5 |
| X | Y | Z |
|---|---|---|
| 62.74 | 47.0007 | 30.8003 |
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 |
| C4' | CD1 | ILE- 268 | 4.31 | 0 | Hydrophobic |
| C20 | CG2 | ILE- 268 | 3.71 | 0 | Hydrophobic |
| C1' | CG2 | ILE- 268 | 4.02 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 268 | 3.68 | 0 | Hydrophobic |
| C20 | CB | ALA- 271 | 3.49 | 0 | Hydrophobic |
| C19 | CZ3 | TRP- 305 | 3.7 | 0 | Hydrophobic |
| C19 | CB | ASN- 306 | 3.84 | 0 | Hydrophobic |
| C2' | CG1 | ILE- 310 | 4.35 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 310 | 4.46 | 0 | Hydrophobic |
| C2' | CE2 | PHE- 313 | 3.58 | 0 | Hydrophobic |
| C1' | CZ | PHE- 313 | 3.41 | 0 | Hydrophobic |
| C20 | CD2 | PHE- 313 | 4.33 | 0 | Hydrophobic |
| O1 | NH2 | ARG- 316 | 3.14 | 133.35 | H-Bond (Protein Donor) |
| O1 | NH1 | ARG- 316 | 2.82 | 147.07 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 316 | 3.4 | 0 | Ionic (Protein Cationic) |
| C20 | CD2 | LEU- 326 | 4.05 | 0 | Hydrophobic |
| O2 | N | ALA- 327 | 3.19 | 178.91 | H-Bond (Protein Donor) |
| C3 | CG1 | VAL- 342 | 3.96 | 0 | Hydrophobic |
| C4 | CG2 | ILE- 345 | 4.17 | 0 | Hydrophobic |
| C4' | CD1 | PHE- 346 | 3.46 | 0 | Hydrophobic |
| C19 | CB | CYS- 432 | 4.05 | 0 | Hydrophobic |
| C18 | SG | CYS- 432 | 3.95 | 0 | Hydrophobic |
| C2 | CB | HIS- 435 | 4.49 | 0 | Hydrophobic |
| C1 | CG | LEU- 436 | 4.28 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 436 | 4.06 | 0 | Hydrophobic |
