Table 2.
Characteristics of PPARγ complexes with fatty acidsa
| Complex | BSA (Å2) | HADDOCK scoreb (AU) | Ligand RMSDc (Å) | Size of clusterd |
|---|---|---|---|---|
| 3U9Q | 478 ± 6 | −22.1 ± 2.9 | 0.0 | NA |
| Cluster 1-butyrate | 286 ± 14 | −7 ± 3 | 1.55 ± 0.29 | 179 |
| Cluster 2-butyrate | 280 ± 6 | 0.1 ± 4 | 4.70 ± 0.77 | 13 |
| Cluster 3-butyrate | 275 ± 6 | 4.6 ± 4 | 1.99 0.13 | 6 |
a
Averages and standard deviations calculated from the best four members (in terms of HADDOCK score) of a set of structures are reported. 3U9Q is the HADDOCK-refined crystal structures of the PPARγ-decanoic acid complex, while the other three clusters were obtained by HADDOCK modeling of the butyrate-PPARγ complex. NA, not applicable.
b
HADDOCK score as defined in Materials and Methods.
c
Positional RMSD of the ligand atoms calculated after superimposition of the protein backbone atoms.
4
Number of calculated structures (out of 200 total) that were clustered together.