sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.640 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: | 23.366 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.305 | 371.250 |
| % Hydrophobic | % Polar |
|---|---|
| 64.55 | 35.45 |
| According to VolSite | |
| HET Code: | AOM |
|---|---|
| Formula: | C19H32O2 |
| Molecular weight: | 292.456 g/mol |
| DrugBank ID: | DB03882 |
| Buried Surface Area: | 59.84 % |
| Polar Surface area: | 40.46 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 15.3923 | -16.7037 | -4.78552 |
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 |
| C1 | CE2 | TYR- 26 | 4.07 | 0 | Hydrophobic |
| C11 | CZ | TYR- 26 | 3.65 | 0 | Hydrophobic |
| C19 | CE1 | TYR- 26 | 4.17 | 0 | Hydrophobic |
| C2 | CG | TYR- 26 | 3.83 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 57 | 4.32 | 0 | Hydrophobic |
| O3 | OH | TYR- 58 | 2.54 | 152.55 | H-Bond (Protein Donor) |
| C2 | CE1 | TYR- 58 | 3.73 | 0 | Hydrophobic |
| C6 | CH2 | TRP- 89 | 4.2 | 0 | Hydrophobic |
| O3 | NE2 | HIS- 120 | 2.8 | 159.56 | H-Bond (Ligand Donor) |
| C18 | CZ | TYR- 132 | 3.38 | 0 | Hydrophobic |
| C8 | CE2 | TYR- 132 | 4.36 | 0 | Hydrophobic |
| C1 | CH2 | TRP- 230 | 3.9 | 0 | Hydrophobic |
| C11 | CE2 | TRP- 230 | 3.99 | 0 | Hydrophobic |
| C12 | CD2 | TRP- 230 | 3.89 | 0 | Hydrophobic |
| C9 | CD2 | TRP- 230 | 4.01 | 0 | Hydrophobic |
| C17 | CB | TRP- 230 | 3.75 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 311 | 3.89 | 0 | Hydrophobic |
| C15 | CE | MET- 313 | 4.45 | 0 | Hydrophobic |
| C7 | CH2 | TRP- 314 | 3.8 | 0 | Hydrophobic |
| C2 | C5N | NAP- 401 | 4.06 | 0 | Hydrophobic |
| C3 | C4N | NAP- 401 | 3.21 | 0 | Hydrophobic |
