sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.150 Å
X-ray
2002-06-17
| Name: | Nuclear receptor subfamily 1 group I member 2 |
|---|---|
| ID: | NR1I2_HUMAN |
| AC: | O75469 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 38.177 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.681 | 1228.500 |
| % Hydrophobic | % Polar |
|---|---|
| 64.01 | 35.99 |
| According to VolSite | |
| HET Code: | HYF |
|---|---|
| Formula: | C35H51O4 |
| Molecular weight: | 535.777 g/mol |
| DrugBank ID: | DB01892 |
| Buried Surface Area: | 64.37 % |
| Polar Surface area: | 74.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 10.3949 | 76.0965 | -1.22649 |
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 | CG | LEU- 206 | 4.34 | 0 | Hydrophobic |
| C3 | CB | LEU- 209 | 3.89 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 209 | 4.01 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 209 | 4.22 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 209 | 3.61 | 0 | Hydrophobic |
| C32 | CD2 | LEU- 209 | 4.43 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 211 | 4 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 239 | 4.15 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 240 | 3.32 | 0 | Hydrophobic |
| C2 | CG | MET- 243 | 3.29 | 0 | Hydrophobic |
| C11 | CG | MET- 243 | 3.94 | 0 | Hydrophobic |
| C33 | CB | MET- 243 | 4.25 | 0 | Hydrophobic |
| C35 | SD | MET- 243 | 4.22 | 0 | Hydrophobic |
| C12 | CB | MET- 243 | 3.28 | 0 | Hydrophobic |
| C36 | CG | MET- 246 | 4.04 | 0 | Hydrophobic |
| C12 | CB | SER- 247 | 4.3 | 0 | Hydrophobic |
| C4 | CB | SER- 247 | 3.61 | 0 | Hydrophobic |
| C4 | CB | MET- 250 | 4.25 | 0 | Hydrophobic |
| C6 | CE2 | PHE- 251 | 4.24 | 0 | Hydrophobic |
| C6 | CD1 | PHE- 281 | 3.57 | 0 | Hydrophobic |
| C26 | CE1 | PHE- 281 | 3.63 | 0 | Hydrophobic |
| C6 | SG | CYS- 284 | 3.27 | 0 | Hydrophobic |
| O21 | NE2 | GLN- 285 | 2.71 | 146.5 | H-Bond (Protein Donor) |
| C36 | CE1 | PHE- 288 | 3.75 | 0 | Hydrophobic |
| C38 | CD1 | PHE- 288 | 3.26 | 0 | Hydrophobic |
| C39 | CE2 | PHE- 288 | 4.01 | 0 | Hydrophobic |
| C4 | CE1 | PHE- 288 | 3.78 | 0 | Hydrophobic |
| C23 | CZ2 | TRP- 299 | 3.6 | 0 | Hydrophobic |
| C39 | CD2 | TRP- 299 | 3.73 | 0 | Hydrophobic |
| C39 | CD1 | TYR- 306 | 4.19 | 0 | Hydrophobic |
| C22 | CG | MET- 323 | 3.96 | 0 | Hydrophobic |
| C23 | CG | MET- 323 | 3.73 | 0 | Hydrophobic |
| C26 | SD | MET- 323 | 3.66 | 0 | Hydrophobic |
| O20 | ND1 | HIS- 407 | 2.59 | 159.72 | H-Bond (Protein Donor) |
| C13 | CD1 | ILE- 414 | 3.41 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 414 | 3.36 | 0 | Hydrophobic |
| C14 | CZ | PHE- 420 | 3.44 | 0 | Hydrophobic |
