sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.090 Å
X-ray
2015-09-23
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.000 | 9.190 | 9.680 | 0.760 | 9.800 | 18 |
| Name: | Estrogen receptor |
|---|---|
| ID: | ESR1_HUMAN |
| AC: | P03372 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 36.739 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.737 | 327.375 |
| % Hydrophobic | % Polar |
|---|---|
| 81.44 | 18.56 |
| According to VolSite | |
| HET Code: | EST |
|---|---|
| Formula: | C18H24O2 |
| Molecular weight: | 272.382 g/mol |
| DrugBank ID: | DB00783 |
| Buried Surface Area: | 75.34 % |
| 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 |
|---|---|---|
| 52.038 | 6.39565 | 89.803 |
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 |
| C12 | CB | LEU- 346 | 4.16 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 349 | 4.07 | 0 | Hydrophobic |
| C11 | CB | ALA- 350 | 4.23 | 0 | Hydrophobic |
| C1 | CB | ALA- 350 | 3.96 | 0 | Hydrophobic |
| O3 | OE1 | GLU- 353 | 2.71 | 135.74 | H-Bond (Ligand Donor) |
| C6 | CD1 | LEU- 384 | 4.41 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 384 | 4.14 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 384 | 4.11 | 0 | Hydrophobic |
| C4 | CB | LEU- 387 | 3.86 | 0 | Hydrophobic |
| C6 | CG | MET- 388 | 3.74 | 0 | Hydrophobic |
| C7 | CE | MET- 388 | 4.23 | 0 | Hydrophobic |
| C15 | CE | MET- 388 | 4.14 | 0 | Hydrophobic |
| C4 | CB | LEU- 391 | 4.05 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 391 | 4.03 | 0 | Hydrophobic |
| O3 | NH2 | ARG- 394 | 3.12 | 152.58 | H-Bond (Protein Donor) |
| C9 | CE1 | PHE- 404 | 4.06 | 0 | Hydrophobic |
| C7 | CE1 | PHE- 404 | 4.25 | 0 | Hydrophobic |
| C15 | CE | MET- 421 | 3.79 | 0 | Hydrophobic |
| C16 | CE | MET- 421 | 3.5 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 424 | 4.2 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 424 | 4.19 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 428 | 4.4 | 0 | Hydrophobic |
| O17 | ND1 | HIS- 524 | 2.89 | 169.98 | H-Bond (Ligand Donor) |
| C18 | CB | LEU- 525 | 4.23 | 0 | Hydrophobic |
| O3 | O | HOH- 1114 | 2.98 | 179.96 | H-Bond (Protein Donor) |
