sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
1998-03-25
| 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: | 32.111 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.461 | 1177.875 |
| % Hydrophobic | % Polar |
|---|---|
| 49.28 | 50.72 |
| According to VolSite | |
| HET Code: | AND |
|---|---|
| Formula: | C19H28O2 |
| Molecular weight: | 288.424 g/mol |
| DrugBank ID: | DB01708 |
| Buried Surface Area: | 61.04 % |
| Polar Surface area: | 37.29 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 10.8757 | 8.14286 | -11.9273 |
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 | 3.33 | 172.52 | H-Bond (Protein Donor) |
| C11 | CG2 | VAL- 143 | 3.34 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 149 | 4.4 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 149 | 3.85 | 0 | Hydrophobic |
| C19 | CG | LEU- 149 | 3.28 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 149 | 3.81 | 0 | Hydrophobic |
| C18 | CE2 | TYR- 155 | 3.62 | 0 | Hydrophobic |
| C15 | CB | PRO- 187 | 4.48 | 0 | Hydrophobic |
| C14 | CE | MET- 193 | 3.52 | 0 | Hydrophobic |
| C7 | CE | MET- 193 | 4.16 | 0 | Hydrophobic |
| C15 | SD | MET- 193 | 3.36 | 0 | Hydrophobic |
| C4 | CE1 | TYR- 218 | 4.15 | 0 | Hydrophobic |
| C7 | CB | SER- 222 | 4.04 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 225 | 3.77 | 0 | Hydrophobic |
| C1 | CZ | PHE- 259 | 3.88 | 0 | Hydrophobic |
| C2 | CE1 | PHE- 259 | 4.1 | 0 | Hydrophobic |
| C2 | CE | MET- 279 | 4.24 | 0 | Hydrophobic |
| O3 | OE2 | GLU- 282 | 3.02 | 159.2 | H-Bond (Ligand Donor) |
