2EW5

Structure of Helicobacter Pylori peptide deformylase in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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.

(2006) Protein Sci. 15: 2071-2081

  • DOI: 10.1110/ps.062238406
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 target ...

    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.


    Organizational Affiliation

    Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica Graduate School of Chinese Academy of Sciences, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
peptide deformylase
A
181Helicobacter pyloriMutation(s): 0 
Gene Names: def
EC: 3.5.1.88
Find proteins for Q672W7 (Helicobacter pylori)
Go to UniProtKB:  Q672W7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Y12
Query on Y12

Download SDF File 
Download CCD File 
A
4-{(1E)-3-OXO-3-[(2-PHENYLETHYL)AMINO]PROP-1-EN-1-YL}-1,2-PHENYLENE DIACETATE
C21 H21 N O5
GARHCDOTUULBOQ-PKNBQFBNSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Y12IC50: 1250 nM BINDINGMOAD
Y12IC50: 1250 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.117α = 90.00
b = 52.970β = 90.00
c = 92.259γ = 90.00
Software Package:
Software NamePurpose
TRUNCATEdata reduction
CNSrefinement
CNSphasing
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2005-11-02 
  • Released Date: 2006-10-24 
  • Deposition Author(s): Cai, J.

Revision History 

  • Version 1.0: 2006-10-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description