sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.630 Å
X-ray
2003-09-12
| 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: | 31.675 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.398 | 455.625 |
| % Hydrophobic | % Polar |
|---|---|
| 57.04 | 42.96 |
| According to VolSite | |
| HET Code: | 5SD |
|---|---|
| Formula: | C19H28O2 |
| Molecular weight: | 288.424 g/mol |
| DrugBank ID: | DB01561 |
| Buried Surface Area: | 51.19 % |
| Polar Surface area: | 34.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 10.9451 | 8.55929 | -12.5101 |
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 |
| C6 | CG1 | VAL- 143 | 3.27 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 149 | 4.44 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 149 | 4.2 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 149 | 3.89 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 149 | 3.77 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 149 | 3.82 | 0 | Hydrophobic |
| C5 | CB | PRO- 187 | 4.07 | 0 | Hydrophobic |
| C11 | CE1 | TYR- 218 | 4.36 | 0 | Hydrophobic |
| C18 | CE1 | TYR- 218 | 4.21 | 0 | Hydrophobic |
| O17 | NE2 | HIS- 221 | 2.56 | 128.23 | H-Bond (Protein Donor) |
| C11 | CB | SER- 222 | 3.85 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 225 | 4.47 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 225 | 4.01 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 225 | 4.41 | 0 | Hydrophobic |
| C7 | CZ | PHE- 259 | 4.03 | 0 | Hydrophobic |
| C15 | CE2 | PHE- 259 | 3.76 | 0 | Hydrophobic |
| C18 | SD | MET- 279 | 4.38 | 0 | Hydrophobic |
| C16 | CE | MET- 279 | 4.03 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 283 | 4.01 | 0 | Hydrophobic |
