sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2003-07-03
| Name: | Retinoic acid receptor RXR-beta |
|---|---|
| ID: | RXRB_HUMAN |
| AC: | P28702 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 22.211 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.974 | 475.875 |
| % Hydrophobic | % Polar |
|---|---|
| 80.14 | 19.86 |
| According to VolSite | |
| HET Code: | MEI |
|---|---|
| Formula: | C16H27O3 |
| Molecular weight: | 267.384 g/mol |
| DrugBank ID: | DB08175 |
| Buried Surface Area: | 70.73 % |
| Polar Surface area: | 49.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 45.2634 | -8.16053 | 29.6566 |
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 |
| C1 | CD1 | ILE- 339 | 4.32 | 0 | Hydrophobic |
| C5 | CG2 | ILE- 339 | 3.77 | 0 | Hydrophobic |
| C10 | CG2 | ILE- 339 | 3.92 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 339 | 3.51 | 0 | Hydrophobic |
| C10 | CB | ALA- 343 | 3.77 | 0 | Hydrophobic |
| C14 | CB | ALA- 343 | 3.42 | 0 | Hydrophobic |
| C9 | CZ3 | TRP- 376 | 4.27 | 0 | Hydrophobic |
| C9 | CB | ASN- 377 | 4.08 | 0 | Hydrophobic |
| C9 | CB | LEU- 380 | 3.73 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 380 | 3.52 | 0 | Hydrophobic |
| C9 | CG1 | ILE- 381 | 3.72 | 0 | Hydrophobic |
| C7 | CE2 | PHE- 384 | 4.02 | 0 | Hydrophobic |
| C9 | CE2 | PHE- 384 | 4.45 | 0 | Hydrophobic |
| O2 | NH2 | ARG- 387 | 2.69 | 120.53 | H-Bond (Protein Donor) |
| O3 | N | ALA- 398 | 3.31 | 155.58 | H-Bond (Protein Donor) |
| C1 | CG2 | VAL- 413 | 3.45 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 413 | 4.47 | 0 | Hydrophobic |
| C1 | CD1 | ILE- 416 | 4.01 | 0 | Hydrophobic |
| C1 | CD1 | PHE- 417 | 4.49 | 0 | Hydrophobic |
| C4 | CB | CYS- 503 | 3.76 | 0 | Hydrophobic |
| C6 | CB | CYS- 503 | 3.59 | 0 | Hydrophobic |
| C4 | CB | HIS- 506 | 3.93 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 507 | 4.29 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 507 | 4.09 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 507 | 3.66 | 0 | Hydrophobic |
