sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2007-06-22
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.920 | 7.940 | 7.940 | 0.020 | 7.960 | 2 |
| 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: | 45.986 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.831 | 462.375 |
| % Hydrophobic | % Polar |
|---|---|
| 76.64 | 23.36 |
| According to VolSite | |
| HET Code: | JJ3 |
|---|---|
| Formula: | C20H22O4 |
| Molecular weight: | 326.386 g/mol |
| DrugBank ID: | DB08020 |
| Buried Surface Area: | 69.43 % |
| Polar Surface area: | 58.92 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 20.4929 | 13.5027 | 30.7584 |
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 |
| O21 | O | HOH- 4 | 3.19 | 144.33 | H-Bond (Protein Donor) |
| C16 | CE | MET- 343 | 3.47 | 0 | Hydrophobic |
| C23 | CB | LEU- 346 | 4.27 | 0 | Hydrophobic |
| C13 | CB | LEU- 346 | 3.97 | 0 | Hydrophobic |
| C12 | CG2 | THR- 347 | 3.76 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 349 | 4.21 | 0 | Hydrophobic |
| C10 | CB | ALA- 350 | 3.47 | 0 | Hydrophobic |
| C23 | CB | ALA- 350 | 3.81 | 0 | Hydrophobic |
| O21 | OE2 | GLU- 353 | 3.24 | 121.95 | H-Bond (Ligand Donor) |
| O21 | OE1 | GLU- 353 | 2.84 | 121.79 | H-Bond (Ligand Donor) |
| C11 | CZ3 | TRP- 383 | 4.11 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 384 | 4.23 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 387 | 4.17 | 0 | Hydrophobic |
| C19 | CB | LEU- 387 | 3.69 | 0 | Hydrophobic |
| C24 | CE | MET- 388 | 3.85 | 0 | Hydrophobic |
| C19 | CB | LEU- 391 | 4.33 | 0 | Hydrophobic |
| O21 | NH2 | ARG- 394 | 2.81 | 129.16 | H-Bond (Protein Donor) |
| C26 | CE1 | PHE- 404 | 3.68 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 424 | 4.44 | 0 | Hydrophobic |
| C24 | CG2 | ILE- 424 | 3.95 | 0 | Hydrophobic |
| C26 | CD1 | LEU- 428 | 3.61 | 0 | Hydrophobic |
| C2 | CB | HIS- 524 | 4.46 | 0 | Hydrophobic |
| O27 | ND1 | HIS- 524 | 2.6 | 140.21 | H-Bond (Ligand Donor) |
| C11 | CD1 | LEU- 525 | 3.81 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 525 | 3.62 | 0 | Hydrophobic |
| C16 | CG | LEU- 525 | 3.78 | 0 | Hydrophobic |
