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
2004-09-07
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.160 | 8.160 | 8.160 | 0.000 | 8.160 | 1 |
| Name: | Retinoic acid receptor beta |
|---|---|
| ID: | RARB_MOUSE |
| AC: | P22605 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 67.572 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.687 | 546.750 |
| % Hydrophobic | % Polar |
|---|---|
| 79.01 | 20.99 |
| According to VolSite | |
| HET Code: | REA |
|---|---|
| Formula: | C20H27O2 |
| Molecular weight: | 299.427 g/mol |
| DrugBank ID: | DB00755 |
| Buried Surface Area: | 72.16 % |
| 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 |
|---|---|---|
| 18.9255 | 31.798 | 102.615 |
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 |
| C3 | CZ3 | TRP- 218 | 4.07 | 0 | Hydrophobic |
| C17 | CZ | PHE- 221 | 3.81 | 0 | Hydrophobic |
| C3 | CE2 | PHE- 221 | 4.14 | 0 | Hydrophobic |
| C20 | CB | LEU- 224 | 4.32 | 0 | Hydrophobic |
| C18 | CB | ALA- 225 | 3.87 | 0 | Hydrophobic |
| C20 | CB | ALA- 225 | 4.2 | 0 | Hydrophobic |
| C20 | CB | CYS- 228 | 3.73 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 259 | 3.97 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 262 | 3.68 | 0 | Hydrophobic |
| C19 | CB | LEU- 262 | 4.09 | 0 | Hydrophobic |
| C19 | CG1 | ILE- 263 | 3.45 | 0 | Hydrophobic |
| C19 | CG2 | ILE- 266 | 4.3 | 0 | Hydrophobic |
| C20 | CD2 | PHE- 279 | 3.96 | 0 | Hydrophobic |
| O1 | OG | SER- 280 | 3.02 | 170.64 | H-Bond (Protein Donor) |
| O2 | N | SER- 280 | 3.02 | 167.26 | H-Bond (Protein Donor) |
| C17 | CG | PHE- 295 | 4.14 | 0 | Hydrophobic |
| C19 | CE1 | PHE- 295 | 3.53 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 298 | 3.38 | 0 | Hydrophobic |
| C2 | CG | ARG- 387 | 4.36 | 0 | Hydrophobic |
| C16 | CG | ARG- 387 | 3.93 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 388 | 4.4 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 403 | 4.12 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 407 | 3.98 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 407 | 3.91 | 0 | Hydrophobic |
