9JSY | pdb_00009jsy

Crystal structure of dehydrogenase/isomerase FabX from Helicobacter pylori in complex with inhibitor 1991


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.195 (Depositor), 0.194 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

Starting Model: experimental
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Literature

Antagonist Targeting the Species-Specific Fatty Acid Dehydrogenase/Isomerase FabX for Anti-H. pylori Infection.

Zhang, L.Ruan, X.Hang, X.Heng, D.Cai, C.Zeng, L.Zhang, G.Zhou, L.Bi, H.Zhang, L.

(2025) Adv Sci (Weinh) 12: e2414844-e2414844

  • DOI: https://doi.org/10.1002/advs.202414844
  • Primary Citation of Related Structures:  
    9JSY, 9K7H

  • PubMed Abstract: 

    Helicobacter pylori (H. pylori) is a group-1 definite pathogenic carcinogen that infects approximately half of the global population, yet no species-specific chemotherapy has yet been developed. It is previously discovered that H. pylori encodes an atypical dehydrogenase/isomerase FabX in the Type-II fatty acid biosynthesis pathway to produce unsaturated fatty acids (UFA) as well as superoxide (ROS). Here, it is demonstrated that FabX is essential for H. pylori growth and gastric colonization by retaining UFA synthesis and producing ROS, respectively, and is a species-specific anti-H. pylori drug target. The first small molecule inhibitor FBX-1991 against FabX, which inhibits the enzymatic activity with an IC 50 value of 0.158 × 10 -6 m in vitro, is developed. FBX-1991 binds inside the catalytic tunnel of FabX, disrupts the conformation of the key catalytic loop, and prevents the insertion of the acyl substrate for catalysis. Further in vivo studies suggest that FBX-1991 inhibits the H. pylori growth by partially inhibiting UFA synthesis and ROS excretion through targeting FabX. This study identifies a species-specific anti-H. pylori drug target, FabX, and discovers the first highly potent and selective FabX inhibitor against H. pylori infection, which provides the molecular basis for developing species-specific anti-H. pylori chemotherapy.


  • Organizational Affiliation
    • Department of Pharmacology and Chemical Biology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-nitropropane dioxygenase365Helicobacter pyloriMutation(s): 0 
Gene Names: B0X24_07955C2840_03950C2842_03950DD776_04195ECB91_05230ECC12_03705SE88_03940
UniProt
Find proteins for A0A0B2E3F3 (Helicobacter pylori)
Explore A0A0B2E3F3 
Go to UniProtKB:  A0A0B2E3F3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B2E3F3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.195 (Depositor), 0.194 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.983α = 90
b = 65.538β = 98.29
c = 53.284γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22477077
National Natural Science Foundation of China (NSFC)China22077081

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release