View source for 2ew6

[[Image:2ew6.jpg|left|200px]]

<!--
The line below this paragraph, containing "STRUCTURE_2ew6", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet) 
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->
{{STRUCTURE_2ew6|  PDB=2ew6  |  SCENE=  }} 

'''Structure of Helicobacter Pylori peptide deformylase in complex with inhibitor'''


==Overview==
Colonization of human stomach by the bacterium Helicobacter pylori is a major causative factor for gastrointestinal illnesses and gastric cancer. However, the discovery of anti-H. pylori agents is a difficult task due to lack of mature protein targets. Therefore, identifying new molecular targets for developing new drugs against H. pylori is obviously necessary. In this study, the in-house potential drug target database (PDTD, http://www.dddc.ac.cn/tarfisdock/) was searched by the reverse docking approach using an active natural product (compound 1) discovered by anti-H. pylori screening as a probe. Homology search revealed that, among the 15 candidates discovered by reverse docking, only diaminopimelate decarboxylase (DC) and peptide deformylase (PDF) have homologous proteins in the genome of H. pylori. Enzymatic assay demonstrated compound 1 and its derivative compound 2 are the potent inhibitors against H. pylori PDF (HpPDF) with IC50 values of 10.8 and 1.25 microM, respectively. X-ray crystal structures of HpPDF and the complexes of HpPDF with 1 and 2 were determined for the first time, indicating that these two inhibitors bind well with HpPDF binding pocket. All these results indicate that HpPDF is a potential target for screening new anti-H. pylori agents. In addition, compounds 1 and 2 were predicted to bind to HpPDF with relatively high selectivity, suggesting they can be used as leads for developing new anti-H. pylori agents. The results demonstrated that our strategy, reverse docking in conjunction with bioassay and structural biology, is effective and can be used as a complementary approach of functional genomics and chemical biology in target identification.

==About this Structure==
2EW6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EW6 OCA]. 

==Reference==
Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking, enzymatic assay, and X-ray crystallography validation., Cai J, Han C, Hu T, Zhang J, Wu D, Wang F, Liu Y, Ding J, Chen K, Yue J, Shen X, Jiang H, Protein Sci. 2006 Sep;15(9):2071-81. Epub 2006 Aug 1. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16882991 16882991]
[[Category: Helicobacter pylori]]
[[Category: Peptide deformylase]]
[[Category: Single protein]]
[[Category: Cai, J.]]
[[Category: Cobalt helicobacter pylori peptide deformylase]]
[[Category: Inhibitor]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 03:11:03 2008''