Docking studies of nickel-peptide deformylase (PDF) inhibitors: exploring the new binding pockets.
The binding modes of a series of known activity inhibitors docking to Peptide deformylase (PDF) have been studied using molecular docking software AutoDock3.0.5. In this study, good correlation (R(2)=0.894) between calculated binding energies and experimental inhibitory activities is obtained. We find that some shallow pockets near the known active pocket are very important which can accommodate the side-chains of the inhibitor. Moreover, a new binding pocket is also explored. All these may provide something useful for designing the potent inhibitors.
Institute of Theoretical Chemistry, Shandong University, Jinan 250100, China.
Qiang
Q
Wang
Datong
D
Zhang
Jianwu
J
Wang
Zhengting
Z
Cai
Weiren
W
Xu
D000581:Amidohydrolases / Q000037:antagonists & inhibitors / Q000737:chemistry*; D001665:Binding Sites; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D006877:Hydroxamic Acids / Q000737:chemistry; D006898:Hydroxylamines / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D009532:Nickel / Q000737:chemistry*; D011487:Protein Conformation; D012984:Software; D013329:Structure-Activity Relationship
D004791:Enzyme Inhibitors; D006877:Hydroxamic Acids; D006898:Hydroxylamines; C513178:n-formylhydroxylamine; D009532:Nickel; D000581:Amidohydrolases; C084507:peptide deformylase