sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.030 Å
X-ray
2008-03-29
| 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: | 29.432 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.187 | 489.375 |
| % Hydrophobic | % Polar |
|---|---|
| 58.62 | 41.38 |
| According to VolSite | |
| HET Code: | STR |
|---|---|
| Formula: | C21H30O2 |
| Molecular weight: | 314.462 g/mol |
| DrugBank ID: | DB00396 |
| Buried Surface Area: | 61.75 % |
| 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 |
|---|---|---|
| 14.9985 | -16.3753 | -5.60178 |
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 | CD2 | TYR- 26 | 3.96 | 0 | Hydrophobic |
| C7 | CZ | TYR- 26 | 3.53 | 0 | Hydrophobic |
| O3 | OH | TYR- 58 | 2.61 | 158.88 | H-Bond (Protein Donor) |
| C1 | CZ3 | TRP- 89 | 4.12 | 0 | Hydrophobic |
| C2 | CG | GLU- 120 | 3.94 | 0 | Hydrophobic |
| C12 | CE2 | TYR- 132 | 3.84 | 0 | Hydrophobic |
| C21 | CZ | TYR- 132 | 4.29 | 0 | Hydrophobic |
| C17 | CZ | TYR- 132 | 4.02 | 0 | Hydrophobic |
| C21 | CH2 | TRP- 140 | 3.89 | 0 | Hydrophobic |
| C6 | CH2 | TRP- 230 | 3.92 | 0 | Hydrophobic |
| C7 | CZ2 | TRP- 230 | 4.33 | 0 | Hydrophobic |
| C8 | CD2 | TRP- 230 | 4.3 | 0 | Hydrophobic |
| C15 | CD2 | TRP- 230 | 4.3 | 0 | Hydrophobic |
| C18 | CB | TRP- 230 | 3.34 | 0 | Hydrophobic |
| C19 | CZ3 | TRP- 230 | 4.16 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 309 | 4.31 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 311 | 4.5 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 311 | 4.05 | 0 | Hydrophobic |
| C18 | CE | MET- 313 | 4.19 | 0 | Hydrophobic |
| C21 | CE | MET- 313 | 4.24 | 0 | Hydrophobic |
| C12 | CH2 | TRP- 314 | 3.76 | 0 | Hydrophobic |
| C2 | C3N | NAP- 3902 | 4.21 | 0 | Hydrophobic |
| C6 | C5N | NAP- 3902 | 4.27 | 0 | Hydrophobic |
| C19 | C4N | NAP- 3902 | 4.13 | 0 | Hydrophobic |
