3DOY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1021/jm8015602
  • Primary Citation of Related Structures:  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 investigate ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
(3R)-hydroxymyristoyl-acyl carrier protein dehydratase
A, B, C, D, E, F
159Helicobacter pyloriGene Names: fabZ
EC: 4.2.1.59
Find proteins for Q5G940 (Helicobacter pylori)
Go to UniProtKB:  Q5G940
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2BE
Query on 2BE

Download SDF File 
Download CCD File 
A, C
4-chloro-N'-[(1E)-(3,5-dibromo-2,4-dihydroxyphenyl)methylidene]benzohydrazide
C14 H9 Br2 Cl N2 O3
ZDMUFSJTENTNDA-NGYBGAFCSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BEN
Query on BEN

Download SDF File 
Download CCD File 
A, B, C, E
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2BEIC50: 1520 nM (97) BINDINGDB
2BEIC50: 1520 nM BINDINGMOAD
2BEIC50: 1520 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.975α = 90.00
b = 100.370β = 90.00
c = 186.622γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
CNSrefinement
CrystalCleardata reduction
SCALAdata scaling
MOSFLMdata reduction
DENZOdata reduction
MOLREPphasing
CrystalCleardata collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description