sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2012-02-07
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.000 | 7.940 | 7.960 | 0.930 | 9.300 | 7 |
| Name: | Retinoic acid receptor beta |
|---|---|
| ID: | RARB_HUMAN |
| AC: | P10826 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 28.979 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.821 | 509.625 |
| % Hydrophobic | % Polar |
|---|---|
| 78.15 | 21.85 |
| According to VolSite | |
| HET Code: | REA |
|---|---|
| Formula: | C20H27O2 |
| Molecular weight: | 299.427 g/mol |
| DrugBank ID: | DB00755 |
| Buried Surface Area: | 72.37 % |
| 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 |
|---|---|---|
| -9.11436 | 10.3419 | 47.2111 |
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- 1227 | 4.09 | 0 | Hydrophobic |
| C17 | CE2 | PHE- 1230 | 3.97 | 0 | Hydrophobic |
| C20 | CE1 | PHE- 1230 | 4.45 | 0 | Hydrophobic |
| C20 | CB | LEU- 1233 | 3.97 | 0 | Hydrophobic |
| C18 | CB | ALA- 1234 | 4.12 | 0 | Hydrophobic |
| C20 | CB | ALA- 1234 | 3.82 | 0 | Hydrophobic |
| C20 | CB | CYS- 1237 | 4.05 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 1268 | 4.17 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 1268 | 4.33 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 1271 | 4.02 | 0 | Hydrophobic |
| C19 | CB | LEU- 1271 | 4.01 | 0 | Hydrophobic |
| C19 | CG1 | ILE- 1272 | 3.39 | 0 | Hydrophobic |
| C19 | CG2 | ILE- 1275 | 4.28 | 0 | Hydrophobic |
| O1 | CZ | ARG- 1278 | 3.8 | 0 | Ionic (Protein Cationic) |
| O1 | NH1 | ARG- 1278 | 2.9 | 145.14 | H-Bond (Protein Donor) |
| C20 | CD2 | PHE- 1288 | 3.57 | 0 | Hydrophobic |
| O1 | N | SER- 1289 | 3.03 | 124.51 | H-Bond (Protein Donor) |
| O1 | OG | SER- 1289 | 2.68 | 167.12 | H-Bond (Protein Donor) |
| O2 | N | SER- 1289 | 3.18 | 174.16 | H-Bond (Protein Donor) |
| O2 | OG | SER- 1289 | 3.46 | 131.24 | H-Bond (Protein Donor) |
| C17 | CD2 | PHE- 1304 | 3.99 | 0 | Hydrophobic |
| C19 | CZ | PHE- 1304 | 3.7 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 1307 | 3.92 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 1397 | 4.14 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 1400 | 3.71 | 0 | Hydrophobic |
| C3 | CE | MET- 1408 | 4.35 | 0 | Hydrophobic |
| C4 | CG2 | ILE- 1412 | 4.1 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 1412 | 4.14 | 0 | Hydrophobic |
