sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
1998-01-14
| Name: | Estradiol 17-beta-dehydrogenase 1 |
|---|---|
| ID: | DHB1_HUMAN |
| AC: | P14061 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.1.1.62 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 100 % |
| B-Factor: | 23.439 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.603 | 826.875 |
| % Hydrophobic | % Polar |
|---|---|
| 66.12 | 33.88 |
| According to VolSite | |
| HET Code: | EST |
|---|---|
| Formula: | C18H24O2 |
| Molecular weight: | 272.382 g/mol |
| DrugBank ID: | DB00783 |
| Buried Surface Area: | 57.35 % |
| 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 |
|---|---|---|
| 6.72215 | 56.5283 | 8.56625 |
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 |
| C11 | CB | VAL- 143 | 3.68 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 143 | 4.18 | 0 | Hydrophobic |
| C13 | CB | VAL- 143 | 4.34 | 0 | Hydrophobic |
| C1 | CE | MET- 147 | 4.49 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 149 | 3.29 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 149 | 3.51 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 149 | 3.69 | 0 | Hydrophobic |
| C16 | CE2 | TYR- 155 | 4.24 | 0 | Hydrophobic |
| C18 | CE2 | TYR- 155 | 3.64 | 0 | Hydrophobic |
| O17 | OH | TYR- 155 | 3.48 | 162.61 | H-Bond (Ligand Donor) |
| C14 | CG | PRO- 187 | 4.33 | 0 | Hydrophobic |
| C7 | CG | PRO- 187 | 4.04 | 0 | Hydrophobic |
| C16 | CE2 | PHE- 192 | 4.03 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 225 | 4.36 | 0 | Hydrophobic |
| C7 | CD1 | PHE- 226 | 4.39 | 0 | Hydrophobic |
| C15 | CE1 | PHE- 226 | 4.36 | 0 | Hydrophobic |
| C9 | CE2 | PHE- 259 | 4.28 | 0 | Hydrophobic |
| C2 | CE | MET- 279 | 4.42 | 0 | Hydrophobic |
| C17 | C4N | NAP- 362 | 3.65 | 0 | Hydrophobic |
