sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2012-02-07
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.300 | 8.800 | 8.800 | 0.500 | 9.300 | 4 |
| 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: | 24.055 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.886 | 506.250 |
| % Hydrophobic | % Polar |
|---|---|
| 80.00 | 20.00 |
| According to VolSite | |
| HET Code: | TTB |
|---|---|
| Formula: | C24H27O2 |
| Molecular weight: | 347.470 g/mol |
| DrugBank ID: | DB02877 |
| Buried Surface Area: | 75.49 % |
| Polar Surface area: | 40.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 0 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -9.16108 | 10.5448 | 44.3068 |
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 |
| C18 | CZ3 | TRP- 1227 | 3.86 | 0 | Hydrophobic |
| C18 | CE2 | PHE- 1230 | 3.89 | 0 | Hydrophobic |
| C6 | CB | LEU- 1233 | 4 | 0 | Hydrophobic |
| C16 | CB | ALA- 1234 | 4.35 | 0 | Hydrophobic |
| C18 | CB | ALA- 1234 | 4.01 | 0 | Hydrophobic |
| C19 | CB | ALA- 1234 | 4.44 | 0 | Hydrophobic |
| C5 | CB | ALA- 1234 | 3.78 | 0 | Hydrophobic |
| C7 | CB | CYS- 1237 | 3.77 | 0 | Hydrophobic |
| C9 | SG | CYS- 1237 | 3.68 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 1268 | 4.38 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 1268 | 4.21 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 1268 | 4.17 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 1268 | 4.17 | 0 | Hydrophobic |
| C | CB | LEU- 1271 | 3.79 | 0 | Hydrophobic |
| C11 | CB | LEU- 1271 | 4.27 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 1271 | 3.95 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 1271 | 4.11 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 1271 | 3.77 | 0 | Hydrophobic |
| C | CG1 | ILE- 1272 | 3.99 | 0 | Hydrophobic |
| C12 | CG1 | ILE- 1272 | 4.29 | 0 | Hydrophobic |
| C | CG2 | ILE- 1275 | 3.43 | 0 | Hydrophobic |
| C10 | CB | ILE- 1275 | 3.84 | 0 | Hydrophobic |
| O1 | NH1 | ARG- 1278 | 3.24 | 151.1 | H-Bond (Protein Donor) |
| C6 | CD2 | PHE- 1288 | 3.23 | 0 | Hydrophobic |
| O | N | SER- 1289 | 2.78 | 172.22 | H-Bond (Protein Donor) |
| O | OG | SER- 1289 | 3.14 | 131.14 | H-Bond (Protein Donor) |
| O1 | N | SER- 1289 | 3.34 | 127.91 | H-Bond (Protein Donor) |
| O1 | OG | SER- 1289 | 2.64 | 154.83 | H-Bond (Protein Donor) |
| C | CZ | PHE- 1304 | 4.05 | 0 | Hydrophobic |
| C23 | CB | ARG- 1396 | 4.27 | 0 | Hydrophobic |
| C24 | CG | ARG- 1396 | 3.71 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 1397 | 3.55 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 1397 | 3.7 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 1400 | 3.68 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 1412 | 3.81 | 0 | Hydrophobic |
| C19 | CG2 | ILE- 1412 | 3.68 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 1416 | 4.13 | 0 | Hydrophobic |
