sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2014-05-16
| Name: | Nuclear receptor subfamily 5 group A member 2 |
|---|---|
| ID: | NR5A2_HUMAN |
| AC: | O00482 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 35 % |
| E | 5 % |
| G | 60 % |
| B-Factor: | 32.035 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.903 | 951.750 |
| % Hydrophobic | % Polar |
|---|---|
| 41.13 | 58.87 |
| According to VolSite | |
| HET Code: | CPS |
|---|---|
| Formula: | C32H58N2O7S |
| Molecular weight: | 614.877 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 51.12 % |
| Polar Surface area: | 155.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| -61.9589 | -8.04856 | 18.034 |
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 |
| C13 | CD1 | LEU- 459 | 4.4 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 459 | 4.06 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 459 | 4.1 | 0 | Hydrophobic |
| C12 | CG | GLU- 471 | 3.59 | 0 | Hydrophobic |
| C1 | CB | GLN- 474 | 3.8 | 0 | Hydrophobic |
| C11 | CB | GLN- 474 | 4.27 | 0 | Hydrophobic |
| C3 | CB | GLU- 475 | 3.97 | 0 | Hydrophobic |
| C4 | CG | GLU- 475 | 3.78 | 0 | Hydrophobic |
| C3 | CB | ASN- 478 | 4.34 | 0 | Hydrophobic |
| C10 | CB | ASN- 478 | 3.57 | 0 | Hydrophobic |
| C21 | CB | ALA- 479 | 3.96 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 482 | 4.36 | 0 | Hydrophobic |
| C7 | CG | GLU- 515 | 3.79 | 0 | Hydrophobic |
| C17 | CB | GLU- 515 | 3.65 | 0 | Hydrophobic |
| O3 | OE1 | GLU- 515 | 2.79 | 152.09 | H-Bond (Ligand Donor) |
| C10 | CZ | TYR- 519 | 4.17 | 0 | Hydrophobic |
| C11 | CE2 | TYR- 519 | 3.55 | 0 | Hydrophobic |
| C16 | CD1 | TYR- 519 | 3.51 | 0 | Hydrophobic |
| C18 | CE1 | TYR- 519 | 3.66 | 0 | Hydrophobic |
