sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 Å
X-ray
1999-07-27
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.560 | 8.560 | 8.560 | 0.000 | 8.560 | 1 |
| Name: | Estrogen receptor beta |
|---|---|
| ID: | ESR2_RAT |
| AC: | Q62986 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 47.919 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.848 | 425.250 |
| % Hydrophobic | % Polar |
|---|---|
| 80.16 | 19.84 |
| According to VolSite | |
| HET Code: | RAL |
|---|---|
| Formula: | C28H28NO4S |
| Molecular weight: | 474.591 g/mol |
| DrugBank ID: | DB00481 |
| Buried Surface Area: | 62.62 % |
| Polar Surface area: | 99.44 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 20.6501 | 29.7706 | 9.01447 |
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 | CB | LEU- 253 | 4.14 | 0 | Hydrophobic |
| C19 | CB | THR- 254 | 4.22 | 0 | Hydrophobic |
| C24 | CG2 | THR- 254 | 3.82 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 256 | 4.03 | 0 | Hydrophobic |
| C1 | CB | ALA- 257 | 4.03 | 0 | Hydrophobic |
| C21 | CB | ALA- 257 | 3.51 | 0 | Hydrophobic |
| N26 | OD1 | ASP- 258 | 3.35 | 171.72 | H-Bond (Ligand Donor) |
| N26 | OD1 | ASP- 258 | 3.35 | 0 | Ionic (Ligand Cationic) |
| O3 | OE1 | GLU- 260 | 3.39 | 133.56 | H-Bond (Ligand Donor) |
| O3 | OE2 | GLU- 260 | 2.6 | 151.6 | H-Bond (Ligand Donor) |
| C30 | CD1 | LEU- 261 | 3.42 | 0 | Hydrophobic |
| S6 | SD | MET- 291 | 4.37 | 0 | Hydrophobic |
| C13 | CE | MET- 291 | 3.6 | 0 | Hydrophobic |
| C22 | CE | MET- 291 | 3.75 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 294 | 4.24 | 0 | Hydrophobic |
| C4 | CB | LEU- 294 | 3.94 | 0 | Hydrophobic |
| C22 | CD1 | LEU- 294 | 4.21 | 0 | Hydrophobic |
| S6 | CG | MET- 295 | 4.13 | 0 | Hydrophobic |
| C8 | CE | MET- 295 | 4.36 | 0 | Hydrophobic |
| S6 | CD2 | LEU- 298 | 3.96 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 298 | 3.86 | 0 | Hydrophobic |
| O3 | NH2 | ARG- 301 | 3.03 | 145.71 | H-Bond (Protein Donor) |
| S6 | CE1 | PHE- 311 | 3.94 | 0 | Hydrophobic |
| C10 | CG1 | ILE- 328 | 3.84 | 0 | Hydrophobic |
| C10 | CG2 | ILE- 331 | 3.41 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 335 | 4.21 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 431 | 3.64 | 0 | Hydrophobic |
| C20 | CD1 | LEU- 431 | 3.62 | 0 | Hydrophobic |
