sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
1996-06-28
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 23.108 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.463 | 806.625 |
| % Hydrophobic | % Polar |
|---|---|
| 59.41 | 40.59 |
| According to VolSite | |
| HET Code: | EST |
|---|---|
| Formula: | C18H24O2 |
| Molecular weight: | 272.382 g/mol |
| DrugBank ID: | DB00783 |
| Buried Surface Area: | 60.24 % |
| 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 |
|---|---|---|
| 45.5341 | 5.74585 | 41.4122 |
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 |
| O17 | OG | SER- 142 | 3.16 | 157.63 | H-Bond (Protein Donor) |
| C12 | CG1 | VAL- 143 | 3.24 | 0 | Hydrophobic |
| C2 | CE | MET- 147 | 4.07 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 149 | 4.28 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 149 | 4.38 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 149 | 3.62 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 149 | 4.35 | 0 | Hydrophobic |
| O17 | OH | TYR- 155 | 3.35 | 143.07 | H-Bond (Ligand Donor) |
| C18 | CE2 | TYR- 155 | 4.01 | 0 | Hydrophobic |
| O3 | NE2 | HIS- 221 | 3.13 | 173.61 | H-Bond (Protein Donor) |
| C6 | CB | SER- 222 | 3.62 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 225 | 4.08 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 225 | 4.02 | 0 | Hydrophobic |
| C16 | CZ | PHE- 226 | 4.01 | 0 | Hydrophobic |
| C14 | CE1 | PHE- 226 | 3.45 | 0 | Hydrophobic |
| C11 | CZ | PHE- 259 | 4.5 | 0 | Hydrophobic |
| C1 | CE1 | PHE- 259 | 3.35 | 0 | Hydrophobic |
| C3 | CE | MET- 279 | 3.84 | 0 | Hydrophobic |
