TABLE 3.
Predicted binding mode of FptA ligands by Gold automated docking
|
Ligand
|
Goldscorea
|
r.m.s.d.b
|
H-bondsc
|
BSAd
|
|
|---|---|---|---|---|---|
| L116:N | L117:N | ||||
| Fe-PchI | 63.81 | 0.30 | X | 97.5 | |
| Fe-NeoPchI | 52.57 | X | 94.5 | ||
| Fe-EPchI | 48.72 | 82.3 | |||
a
Goldscore is the fitness function of the GOLD program (34), which quantifies protein-ligand interactions according to four terms: protein-ligand H-bond interaction energy, protein-ligand van der Waals interaction energy, ligand internal van der Waals energy, ligand torsional strain energy. The data concerning Fe-NeoPchI have been published previously (22)
b
Root mean square deviations (in Å) of the heavy atoms from the x-ray configuration of Fe-PchI
c
Possible H-bonds are indicated by an X
d
Buried surface area (in percentage of the total surface) of the FptA-bound ligand