sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.030 Å
X-ray
1999-03-31
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.310 | 9.520 | 9.580 | 0.150 | 9.660 | 3 |
| 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: | 23.400 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.703 | 317.250 |
| % Hydrophobic | % Polar |
|---|---|
| 77.66 | 22.34 |
| According to VolSite | |
| HET Code: | DES |
|---|---|
| Formula: | C18H20O2 |
| Molecular weight: | 268.350 g/mol |
| DrugBank ID: | DB00255 |
| Buried Surface Area: | 76.06 % |
| Polar Surface area: | 40.46 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -2.5969 | -8.17985 | 21.8568 |
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- 54 | 3.19 | 139.71 | H-Bond (Protein Donor) |
| CP4 | SD | MET- 343 | 3.68 | 0 | Hydrophobic |
| CP5 | CB | LEU- 346 | 4.17 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 346 | 4.35 | 0 | Hydrophobic |
| CP5 | CG2 | THR- 347 | 4.27 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 349 | 4.41 | 0 | Hydrophobic |
| CP9 | CB | ALA- 350 | 3.4 | 0 | Hydrophobic |
| C5 | CB | ALA- 350 | 3.94 | 0 | Hydrophobic |
| O3 | OE1 | GLU- 353 | 2.51 | 145.04 | H-Bond (Ligand Donor) |
| O3 | OE2 | GLU- 353 | 3.29 | 127.03 | H-Bond (Ligand Donor) |
| CP8 | CD1 | LEU- 384 | 3.8 | 0 | Hydrophobic |
| C2 | CB | LEU- 387 | 3.81 | 0 | Hydrophobic |
| C9 | CE | MET- 388 | 4.37 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 391 | 4.04 | 0 | Hydrophobic |
| O3 | NH2 | ARG- 394 | 3.29 | 151.28 | H-Bond (Protein Donor) |
| C8 | CE1 | PHE- 404 | 3.63 | 0 | Hydrophobic |
| C8 | CE | MET- 421 | 4.44 | 0 | Hydrophobic |
| C9 | SD | MET- 421 | 4.4 | 0 | Hydrophobic |
| CP3 | CE | MET- 421 | 3.55 | 0 | Hydrophobic |
| C9 | CG2 | ILE- 424 | 4.22 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 428 | 4.01 | 0 | Hydrophobic |
| CP2 | CB | HIS- 524 | 4.47 | 0 | Hydrophobic |
| CP9 | CD2 | LEU- 525 | 4.17 | 0 | Hydrophobic |
| CP2 | CB | LEU- 525 | 3.8 | 0 | Hydrophobic |
| CP3 | CD1 | LEU- 525 | 3.73 | 0 | Hydrophobic |
| CP9 | CD1 | LEU- 540 | 4.29 | 0 | Hydrophobic |
