Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with compound 3k

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.210 

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Discovering potent inhibitors against the beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) of Helicobacter pylori: structure-based design, synthesis, bioassay, and crystal structure determination.

He, L.Zhang, L.Liu, X.Li, X.Zheng, M.Li, H.Yu, K.Chen, K.Shen, X.Jiang, H.Liu, H.

(2009) J Med Chem 52: 2465-2481

  • DOI: https://doi.org/10.1021/jm8015602
  • Primary Citation of Related Structures:  
    3DOY, 3DOZ, 3DP0, 3DP1, 3DP2, 3DP3

  • PubMed Abstract: 

    The discovery of HpFabZ inhibitors is now of special interest in the treatment of various gastric diseases. In this work, three series of derivatives (compounds 3, 4, and 5) were designed, synthesized, and their biological activities were investigated as potential HpFabZ inhibitors in a two phased manner. First, we designed and synthesized two series of derivatives (3a-r and 4a-u) and evaluated the enzyme-based assay against HpFabZ. Five compounds (3i-k, 3m, and 3q) showed potential inhibitory activity, with IC(50) values less than 2 muM. Second, a focused combinatorial library containing 280 molecules was designed employing the LD1.0 program. Twelve compounds (5a-l) were selected and synthesized. The activity of the most potent compound 5h (IC(50) = 0.86 muM) was 46 times higher than that of the hit 1. The high hit rate and the potency of the new HpFabZ inhibitors demonstrated the efficiency of the strategy for the focused library design and virtual screening.

  • Organizational Affiliation

    Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
(3R)-hydroxymyristoyl-acyl carrier protein dehydratase
A, B, C, D, E
A, B, C, D, E, F
159Helicobacter pyloriMutation(s): 0 
Gene Names: fabZ
EC: 4.2.1
Find proteins for Q5G940 (Helicobacter pylori)
Explore Q5G940 
Go to UniProtKB:  Q5G940
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5G940
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 3BE

Download Ideal Coordinates CCD File 
N [auth B],
Q [auth C]
C14 H9 Br3 N2 O3
Query on BEN

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
L [auth B]
M [auth B]
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
P [auth C]
C7 H8 N2
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]
K [auth B]
O [auth C]
R [auth D]
S [auth E]
G [auth A],
K [auth B],
O [auth C],
R [auth D],
S [auth E],
T [auth F]
Binding Affinity Annotations 
IDSourceBinding Affinity
3BE BindingDB:  3DOZ IC50: 1980 (nM) from 1 assay(s)
Binding MOAD:  3DOZ IC50: 1980 (nM) from 1 assay(s)
PDBBind:  3DOZ IC50: 1980 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.737α = 90
b = 100.215β = 90
c = 186.564γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
SCALAdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection
CrystalCleardata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description