sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2006-08-08
| Name: | Peroxisome proliferator-activated receptor delta |
|---|---|
| ID: | PPARD_HUMAN |
| AC: | Q03181 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 31.185 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.854 | 891.000 |
| % Hydrophobic | % Polar |
|---|---|
| 67.42 | 32.58 |
| According to VolSite | |
| HET Code: | GNI |
|---|---|
| Formula: | C26H19Cl2N2O5 |
| Molecular weight: | 510.345 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 74.08 % |
| Polar Surface area: | 104.49 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -2.64386 | -7.94777 | 0.992057 |
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 |
| CL26 | CD1 | LEU- 219 | 3.49 | 0 | Hydrophobic |
| C28 | CG1 | VAL- 245 | 4.26 | 0 | Hydrophobic |
| C27 | CG1 | VAL- 245 | 3.59 | 0 | Hydrophobic |
| CL26 | CG | ARG- 248 | 3.42 | 0 | Hydrophobic |
| C23 | CB | ARG- 248 | 3.45 | 0 | Hydrophobic |
| C7 | SG | CYS- 249 | 3.85 | 0 | Hydrophobic |
| C2 | CB | CYS- 249 | 4.22 | 0 | Hydrophobic |
| CL29 | SG | CYS- 249 | 3.61 | 0 | Hydrophobic |
| C25 | SG | CYS- 249 | 3.64 | 0 | Hydrophobic |
| C31 | CB | CYS- 249 | 3.53 | 0 | Hydrophobic |
| C5 | CG | GLN- 250 | 4.43 | 0 | Hydrophobic |
| C2 | CG | GLN- 250 | 4.21 | 0 | Hydrophobic |
| C7 | CB | THR- 252 | 3.47 | 0 | Hydrophobic |
| O | OG1 | THR- 253 | 2.87 | 152.08 | H-Bond (Protein Donor) |
| C2 | CG2 | THR- 253 | 3.26 | 0 | Hydrophobic |
| O | NE2 | HIS- 287 | 2.81 | 144.24 | H-Bond (Protein Donor) |
| C17 | CB | LEU- 294 | 4.44 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 294 | 3.33 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 298 | 4.03 | 0 | Hydrophobic |
| C17 | CB | VAL- 298 | 4.5 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 298 | 3.92 | 0 | Hydrophobic |
| C25 | CD1 | LEU- 303 | 4.38 | 0 | Hydrophobic |
| CL29 | CD2 | LEU- 303 | 4.32 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 303 | 3.5 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 305 | 3.8 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 305 | 3.73 | 0 | Hydrophobic |
| C27 | CG1 | VAL- 312 | 4.01 | 0 | Hydrophobic |
| C28 | CG2 | VAL- 312 | 3.87 | 0 | Hydrophobic |
| C27 | CD1 | LEU- 317 | 4.35 | 0 | Hydrophobic |
| CL29 | CD1 | LEU- 317 | 3.63 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 327 | 4.42 | 0 | Hydrophobic |
| C3 | CG2 | ILE- 327 | 4.1 | 0 | Hydrophobic |
| C19 | CB | ILE- 328 | 4.32 | 0 | Hydrophobic |
| C14 | CB | LYS- 331 | 3.47 | 0 | Hydrophobic |
| O3 | NE2 | HIS- 413 | 2.93 | 174.15 | H-Bond (Protein Donor) |
| C3 | CE | MET- 417 | 3.88 | 0 | Hydrophobic |
| C5 | CE | MET- 417 | 3.3 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 433 | 4.32 | 0 | Hydrophobic |
| O3 | OH | TYR- 437 | 2.74 | 140.54 | H-Bond (Protein Donor) |
