sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
1999-07-27
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.620 | 8.420 | 8.420 | 0.800 | 9.230 | 2 |
| Name: | Estrogen receptor beta |
|---|---|
| ID: | ESR2_HUMAN |
| AC: | Q92731 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 34.845 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.505 | 246.375 |
| % Hydrophobic | % Polar |
|---|---|
| 82.19 | 17.81 |
| According to VolSite | |
| HET Code: | GEN |
|---|---|
| Formula: | C15H9O5 |
| Molecular weight: | 269.229 g/mol |
| DrugBank ID: | DB01645 |
| Buried Surface Area: | 80.38 % |
| Polar Surface area: | 89.82 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 22.3886 | 8.1497 | 113.677 |
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 |
| C2 | CE | MET- 295 | 3.48 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 298 | 4.36 | 0 | Hydrophobic |
| C1 | CG2 | THR- 299 | 4.24 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 301 | 3.8 | 0 | Hydrophobic |
| C16 | CB | ALA- 302 | 4.04 | 0 | Hydrophobic |
| O14 | OE2 | GLU- 305 | 3.39 | 130.36 | H-Bond (Ligand Donor) |
| O14 | OE1 | GLU- 305 | 2.6 | 134.35 | H-Bond (Ligand Donor) |
| C5 | CE | MET- 336 | 4.21 | 0 | Hydrophobic |
| C12 | SD | MET- 336 | 4.2 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 339 | 4.37 | 0 | Hydrophobic |
| C13 | CB | LEU- 339 | 3.71 | 0 | Hydrophobic |
| C12 | CG | MET- 340 | 4.16 | 0 | Hydrophobic |
| C13 | CB | LEU- 343 | 4.34 | 0 | Hydrophobic |
| O14 | NH2 | ARG- 346 | 3.02 | 136.28 | H-Bond (Protein Donor) |
| C3 | CD1 | ILE- 373 | 3.81 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 376 | 4.36 | 0 | Hydrophobic |
| O2 | ND1 | HIS- 475 | 2.72 | 158.13 | H-Bond (Ligand Donor) |
| C3 | CB | HIS- 475 | 4.17 | 0 | Hydrophobic |
| C2 | CB | LEU- 476 | 3.9 | 0 | Hydrophobic |
