sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2008-02-20
| 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: | 11.522 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 19 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.001 | 772.875 |
| % Hydrophobic | % Polar |
|---|---|
| 53.28 | 46.72 |
| According to VolSite | |
| HET Code: | CI2 |
|---|---|
| Formula: | C21H32O2 |
| Molecular weight: | 316.478 g/mol |
| DrugBank ID: | DB07557 |
| Buried Surface Area: | 54.64 % |
| 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: | 1 |
| X | Y | Z |
|---|---|---|
| 4.8857 | 36.4427 | -30.6854 |
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 |
| C9 | CZ | TYR- 26 | 3.62 | 0 | Hydrophobic |
| C10 | CE2 | TYR- 26 | 3.81 | 0 | Hydrophobic |
| C12 | CE1 | TYR- 26 | 4.06 | 0 | Hydrophobic |
| C12 | CE2 | TYR- 58 | 4.38 | 0 | Hydrophobic |
| O14 | OH | TYR- 58 | 3.45 | 137.94 | H-Bond (Protein Donor) |
| C15 | CZ3 | TRP- 89 | 4.45 | 0 | Hydrophobic |
| C21 | CE2 | TYR- 132 | 3.88 | 0 | Hydrophobic |
| C1 | CH2 | TRP- 140 | 3.76 | 0 | Hydrophobic |
| C8 | CD2 | TRP- 230 | 4.41 | 0 | Hydrophobic |
| C9 | CE2 | TRP- 230 | 4.2 | 0 | Hydrophobic |
| C10 | CZ2 | TRP- 230 | 3.65 | 0 | Hydrophobic |
| C18 | CZ3 | TRP- 230 | 3.66 | 0 | Hydrophobic |
| C23 | CB | TRP- 230 | 4.2 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 309 | 3.65 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 311 | 3.72 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 311 | 3.64 | 0 | Hydrophobic |
| C1 | CE | MET- 313 | 3.8 | 0 | Hydrophobic |
| C23 | CE | MET- 313 | 3.54 | 0 | Hydrophobic |
| C21 | CH2 | TRP- 314 | 3.51 | 0 | Hydrophobic |
| C11 | C5N | NAP- 327 | 4.17 | 0 | Hydrophobic |
| C16 | C4N | NAP- 327 | 4.24 | 0 | Hydrophobic |
