sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.860 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 |
|---|---|
| A | 100 % |
| B-Factor: | 14.363 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.633 | 330.750 |
| % Hydrophobic | % Polar |
|---|---|
| 77.55 | 22.45 |
| According to VolSite | |
| HET Code: | EST |
|---|---|
| Formula: | C18H24O2 |
| Molecular weight: | 272.382 g/mol |
| DrugBank ID: | DB00783 |
| Buried Surface Area: | 77.21 % |
| 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 |
|---|---|---|
| 24.409 | -1.6493 | 7.08905 |
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 | CE | MET- 343 | 4.16 | 0 | Hydrophobic |
| C17 | CE | MET- 343 | 4.08 | 0 | Hydrophobic |
| C1 | CB | LEU- 346 | 4.48 | 0 | Hydrophobic |
| C11 | CB | LEU- 346 | 3.96 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 349 | 4.01 | 0 | Hydrophobic |
| C1 | CB | ALA- 350 | 4.04 | 0 | Hydrophobic |
| O3 | OE2 | GLU- 353 | 3.32 | 127.61 | H-Bond (Ligand Donor) |
| C6 | CD1 | LEU- 384 | 4.34 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 384 | 4.14 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 384 | 4.2 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 387 | 4.35 | 0 | Hydrophobic |
| C4 | CB | LEU- 387 | 3.82 | 0 | Hydrophobic |
| C6 | CG | MET- 388 | 3.75 | 0 | Hydrophobic |
| C7 | CE | MET- 388 | 4.03 | 0 | Hydrophobic |
| C15 | CE | MET- 388 | 4.23 | 0 | Hydrophobic |
| C4 | CB | LEU- 391 | 4.16 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 391 | 3.93 | 0 | Hydrophobic |
| O3 | NH2 | ARG- 394 | 3.14 | 150.19 | H-Bond (Protein Donor) |
| C9 | CE1 | PHE- 404 | 4.21 | 0 | Hydrophobic |
| C6 | CE1 | PHE- 404 | 4.04 | 0 | Hydrophobic |
| C16 | SD | MET- 421 | 4.29 | 0 | Hydrophobic |
| C17 | CE | MET- 421 | 4.13 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 424 | 4.23 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 424 | 4.15 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 428 | 4.39 | 0 | Hydrophobic |
| C16 | CB | HIS- 524 | 4.06 | 0 | Hydrophobic |
| O17 | ND1 | HIS- 524 | 2.91 | 162.53 | H-Bond (Ligand Donor) |
| C18 | CB | LEU- 525 | 4.03 | 0 | Hydrophobic |
| O3 | O | HOH- 1154 | 3.15 | 131.51 | H-Bond (Protein Donor) |
