sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.620 Å
X-ray
2008-01-03
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 16.927 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.770 | 627.750 |
| % Hydrophobic | % Polar |
|---|---|
| 50.54 | 49.46 |
| According to VolSite | |
| HET Code: | TES |
|---|---|
| Formula: | C19H28O2 |
| Molecular weight: | 288.424 g/mol |
| DrugBank ID: | DB00624 |
| Buried Surface Area: | 73.68 % |
| 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 |
|---|---|---|
| 4.7539 | 22.0237 | -32.9049 |
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 | 3.28 | 0 | Hydrophobic |
| C19 | CD2 | TYR- 26 | 3.28 | 0 | Hydrophobic |
| C11 | CE1 | TYR- 26 | 3.5 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 57 | 4.35 | 0 | Hydrophobic |
| C18 | CE1 | TYR- 58 | 3.83 | 0 | Hydrophobic |
| C16 | CZ3 | TRP- 89 | 3.84 | 0 | Hydrophobic |
| C17 | CH2 | TRP- 89 | 4.13 | 0 | Hydrophobic |
| C17 | CE2 | TYR- 132 | 4.37 | 0 | Hydrophobic |
| O17 | OH | TYR- 132 | 2.64 | 164.89 | H-Bond (Protein Donor) |
| O3 | OG | SER- 225 | 2.89 | 148.92 | H-Bond (Protein Donor) |
| C2 | CB | ASN- 227 | 4.4 | 0 | Hydrophobic |
| O3 | N | ASN- 227 | 3.28 | 163.27 | H-Bond (Protein Donor) |
| C1 | CB | TRP- 230 | 4.28 | 0 | Hydrophobic |
| C7 | CB | TRP- 230 | 4.46 | 0 | Hydrophobic |
| C9 | CD2 | TRP- 230 | 4.11 | 0 | Hydrophobic |
| C11 | CE2 | TRP- 230 | 4.28 | 0 | Hydrophobic |
| C12 | CZ2 | TRP- 230 | 3.73 | 0 | Hydrophobic |
| C14 | CE3 | TRP- 230 | 4.04 | 0 | Hydrophobic |
| C17 | CH2 | TRP- 230 | 3.67 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 309 | 3.43 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 309 | 3.42 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 311 | 4.18 | 0 | Hydrophobic |
| C16 | CZ3 | TRP- 314 | 4.28 | 0 | Hydrophobic |
| C17 | CH2 | TRP- 314 | 4.36 | 0 | Hydrophobic |
| C18 | C4N | NAP- 327 | 4.5 | 0 | Hydrophobic |
| C6 | C5N | NAP- 327 | 3.39 | 0 | Hydrophobic |
| C19 | C5N | NAP- 327 | 3.66 | 0 | Hydrophobic |
| C15 | C4N | NAP- 327 | 4.15 | 0 | Hydrophobic |
