sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2004-09-22
| Name: | Retinoic acid receptor RXR |
|---|---|
| ID: | RXR_BIOGL |
| AC: | Q8T5C6 |
| Organism: | Biomphalaria glabrata |
| Reign: | Eukaryota |
| TaxID: | 6526 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 39.531 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.148 | 695.250 |
| % Hydrophobic | % Polar |
|---|---|
| 64.56 | 35.44 |
| According to VolSite | |
| HET Code: | REA |
|---|---|
| Formula: | C20H27O2 |
| Molecular weight: | 299.427 g/mol |
| DrugBank ID: | DB00755 |
| Buried Surface Area: | 70.58 % |
| 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 |
|---|---|---|
| 33.8661 | 38.6856 | 90.8097 |
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- 242 | 4.22 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 242 | 3.91 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 242 | 4.12 | 0 | Hydrophobic |
| C20 | CG2 | ILE- 242 | 3.73 | 0 | Hydrophobic |
| C8 | CG2 | ILE- 242 | 3.74 | 0 | Hydrophobic |
| C16 | SG | CYS- 243 | 3.82 | 0 | Hydrophobic |
| C14 | CB | ALA- 245 | 4.32 | 0 | Hydrophobic |
| C20 | CB | ALA- 245 | 3.66 | 0 | Hydrophobic |
| C11 | CB | ALA- 246 | 3.75 | 0 | Hydrophobic |
| C14 | CG | GLN- 249 | 3.56 | 0 | Hydrophobic |
| C19 | CZ3 | TRP- 279 | 4.38 | 0 | Hydrophobic |
| C19 | CB | ASN- 280 | 4.29 | 0 | Hydrophobic |
| C11 | CB | LEU- 283 | 4.47 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 284 | 4.05 | 0 | Hydrophobic |
| C8 | CE2 | PHE- 287 | 4.36 | 0 | Hydrophobic |
| C11 | CE2 | PHE- 287 | 3.7 | 0 | Hydrophobic |
| C14 | CD2 | PHE- 287 | 4.25 | 0 | Hydrophobic |
| C18 | CZ | PHE- 287 | 3.77 | 0 | Hydrophobic |
| C20 | CD2 | PHE- 287 | 3.9 | 0 | Hydrophobic |
| O1 | CZ | ARG- 290 | 3.42 | 0 | Ionic (Protein Cationic) |
| O1 | NH2 | ARG- 290 | 2.51 | 158.78 | H-Bond (Protein Donor) |
| C20 | CD1 | LEU- 300 | 3.77 | 0 | Hydrophobic |
| O2 | N | ALA- 301 | 2.86 | 158.26 | H-Bond (Protein Donor) |
| C2 | CG1 | VAL- 316 | 4.09 | 0 | Hydrophobic |
| C3 | CB | VAL- 316 | 3.64 | 0 | Hydrophobic |
| C3 | CG2 | ILE- 319 | 4.07 | 0 | Hydrophobic |
| C4 | CD1 | PHE- 320 | 4.48 | 0 | Hydrophobic |
| C7 | SG | CYS- 406 | 4.06 | 0 | Hydrophobic |
| C17 | CB | CYS- 406 | 4.16 | 0 | Hydrophobic |
| C18 | SG | CYS- 406 | 3.64 | 0 | Hydrophobic |
| C19 | CB | CYS- 406 | 4.06 | 0 | Hydrophobic |
| C17 | CB | HIS- 409 | 3.44 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 410 | 3.74 | 0 | Hydrophobic |
| C17 | CD2 | LEU- 410 | 4.16 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 410 | 4.38 | 0 | Hydrophobic |
| C16 | CE1 | PHE- 413 | 4.23 | 0 | Hydrophobic |
| C17 | CE1 | PHE- 413 | 4.35 | 0 | Hydrophobic |
