sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.820 Å
X-ray
2011-12-07
| Name: | 3-oxo-5-beta-steroid 4-dehydrogenase |
|---|---|
| ID: | AK1D1_HUMAN |
| AC: | P51857 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 29.039 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 19 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.286 | 472.500 |
| % Hydrophobic | % Polar |
|---|---|
| 63.57 | 36.43 |
| According to VolSite | |
| HET Code: | TES |
|---|---|
| Formula: | C19H28O2 |
| Molecular weight: | 288.424 g/mol |
| DrugBank ID: | DB00624 |
| Buried Surface Area: | 58.94 % |
| 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 |
|---|---|---|
| 15.5431 | -16.9012 | -5.22629 |
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 |
| C7 | CZ | TYR- 26 | 3.43 | 0 | Hydrophobic |
| O3 | OH | TYR- 58 | 2.7 | 144.29 | H-Bond (Protein Donor) |
| C1 | CH2 | TRP- 89 | 4.08 | 0 | Hydrophobic |
| C2 | CZ3 | TRP- 89 | 4.26 | 0 | Hydrophobic |
| O3 | NE2 | HIS- 120 | 2.67 | 125.16 | H-Bond (Protein Donor) |
| C14 | CZ | TYR- 132 | 4.22 | 0 | Hydrophobic |
| C11 | CE2 | TYR- 132 | 3.45 | 0 | Hydrophobic |
| C12 | CE2 | TYR- 132 | 3.41 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 229 | 4.11 | 0 | Hydrophobic |
| C6 | CZ2 | TRP- 230 | 3.42 | 0 | Hydrophobic |
| C7 | CE2 | TRP- 230 | 3.82 | 0 | Hydrophobic |
| C8 | CD2 | TRP- 230 | 4.06 | 0 | Hydrophobic |
| C13 | CB | TRP- 230 | 4.47 | 0 | Hydrophobic |
| C15 | CB | TRP- 230 | 4.26 | 0 | Hydrophobic |
| C19 | CE3 | TRP- 230 | 3.8 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 311 | 4.15 | 0 | Hydrophobic |
| C18 | CE | MET- 313 | 3.82 | 0 | Hydrophobic |
| C11 | CH2 | TRP- 314 | 3.83 | 0 | Hydrophobic |
| C2 | C4N | NAP- 401 | 4.3 | 0 | Hydrophobic |
