sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.470 Å
X-ray
2000-07-19
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.130 | 7.130 | 7.130 | 0.000 | 7.130 | 1 |
| Name: | Retinoic acid receptor gamma |
|---|---|
| ID: | RARG_HUMAN |
| AC: | P13631 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 20.591 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.967 | 516.375 |
| % Hydrophobic | % Polar |
|---|---|
| 80.39 | 19.61 |
| According to VolSite | |
| HET Code: | 184 |
|---|---|
| Formula: | C26H27O3 |
| Molecular weight: | 387.491 g/mol |
| DrugBank ID: | DB03466 |
| Buried Surface Area: | 83.63 % |
| Polar Surface area: | 60.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 40.1293 | 15.2666 | 84.149 |
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 |
| C25 | CH2 | TRP- 227 | 3.83 | 0 | Hydrophobic |
| C23 | CE2 | PHE- 230 | 3.75 | 0 | Hydrophobic |
| C12 | CZ | PHE- 230 | 4.06 | 0 | Hydrophobic |
| C11 | CB | LEU- 233 | 4.34 | 0 | Hydrophobic |
| C22 | CB | ALA- 234 | 4.3 | 0 | Hydrophobic |
| C9 | CB | ALA- 234 | 3.71 | 0 | Hydrophobic |
| C2 | CB | CYS- 237 | 3.82 | 0 | Hydrophobic |
| C3 | SG | CYS- 237 | 3.66 | 0 | Hydrophobic |
| C26 | CD1 | LEU- 268 | 4.44 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 268 | 3.96 | 0 | Hydrophobic |
| C22 | CD1 | LEU- 268 | 3.87 | 0 | Hydrophobic |
| C22 | CD1 | LEU- 271 | 4.03 | 0 | Hydrophobic |
| C12 | CB | LEU- 271 | 4.46 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 271 | 3.92 | 0 | Hydrophobic |
| C6 | CB | LEU- 271 | 3.79 | 0 | Hydrophobic |
| C24 | CE | MET- 272 | 3.89 | 0 | Hydrophobic |
| C14 | CE | MET- 272 | 4.24 | 0 | Hydrophobic |
| C12 | SD | MET- 272 | 4.24 | 0 | Hydrophobic |
| C4 | CB | ARG- 274 | 4.11 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 275 | 4.28 | 0 | Hydrophobic |
| C7 | CG2 | ILE- 275 | 4.47 | 0 | Hydrophobic |
| C6 | CB | ILE- 275 | 3.48 | 0 | Hydrophobic |
| C11 | CD2 | PHE- 288 | 3.43 | 0 | Hydrophobic |
| O2 | N | SER- 289 | 2.94 | 160.95 | H-Bond (Protein Donor) |
| C23 | CG | PHE- 304 | 4.22 | 0 | Hydrophobic |
| C24 | CE2 | PHE- 304 | 4.02 | 0 | Hydrophobic |
| C12 | CZ | PHE- 304 | 3.88 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 307 | 4.07 | 0 | Hydrophobic |
| C17 | CG | ARG- 396 | 4.22 | 0 | Hydrophobic |
| C24 | CG | ARG- 396 | 4.31 | 0 | Hydrophobic |
| C26 | CB | ALA- 397 | 4.08 | 0 | Hydrophobic |
| C18 | CB | ALA- 397 | 4.14 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 400 | 4.4 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 400 | 3.69 | 0 | Hydrophobic |
| C18 | CE | MET- 408 | 4.34 | 0 | Hydrophobic |
| C25 | SD | MET- 408 | 4.15 | 0 | Hydrophobic |
| C25 | CG2 | ILE- 412 | 3.7 | 0 | Hydrophobic |
| C26 | CG2 | ILE- 412 | 4.14 | 0 | Hydrophobic |
| C26 | CE | MET- 415 | 3.98 | 0 | Hydrophobic |
| C21 | CE | MET- 415 | 4.26 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 416 | 3.93 | 0 | Hydrophobic |
