sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2010-08-26
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.000 | 9.200 | 9.300 | 0.910 | 10.820 | 14 |
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 15.909 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.565 | 357.750 |
| % Hydrophobic | % Polar |
|---|---|
| 70.75 | 29.25 |
| According to VolSite | |
| HET Code: | EST |
|---|---|
| Formula: | C18H24O2 |
| Molecular weight: | 272.382 g/mol |
| DrugBank ID: | DB00783 |
| Buried Surface Area: | 73.95 % |
| Polar Surface area: | 40.46 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| -25.866 | 28.1776 | -12.9146 |
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 |
| O3 | O | HOH- 67 | 3.07 | 121.35 | H-Bond (Protein Donor) |
| C12 | CE | MET- 295 | 4.44 | 0 | Hydrophobic |
| C17 | CE | MET- 295 | 4.19 | 0 | Hydrophobic |
| C11 | CB | LEU- 298 | 3.91 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 301 | 3.98 | 0 | Hydrophobic |
| C11 | CB | ALA- 302 | 4.48 | 0 | Hydrophobic |
| C1 | CB | ALA- 302 | 4.04 | 0 | Hydrophobic |
| O3 | OE2 | GLU- 305 | 3.48 | 137.41 | H-Bond (Ligand Donor) |
| O3 | OE1 | GLU- 305 | 2.63 | 145.13 | H-Bond (Ligand Donor) |
| C18 | CE | MET- 336 | 3.52 | 0 | Hydrophobic |
| C4 | CB | LEU- 339 | 4.02 | 0 | Hydrophobic |
| C6 | CG | MET- 340 | 3.9 | 0 | Hydrophobic |
| C7 | CE | MET- 340 | 4.25 | 0 | Hydrophobic |
| C15 | CE | MET- 340 | 4.44 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 343 | 4.06 | 0 | Hydrophobic |
| O3 | NH2 | ARG- 346 | 3.3 | 152.93 | H-Bond (Protein Donor) |
| C9 | CE2 | PHE- 356 | 4.29 | 0 | Hydrophobic |
| C7 | CE2 | PHE- 356 | 4.25 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 373 | 4.01 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 376 | 4.11 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 376 | 4.03 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 380 | 4.15 | 0 | Hydrophobic |
| C16 | CB | HIS- 475 | 4.09 | 0 | Hydrophobic |
| O17 | ND1 | HIS- 475 | 3 | 162.27 | H-Bond (Ligand Donor) |
| C18 | CB | LEU- 476 | 4.03 | 0 | Hydrophobic |
