3ED0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.230 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Emodin targets the beta-hydroxyacyl-acyl carrier protein dehydratase from Helicobacter pylori: enzymatic inhibition assay with crystal structural and thermodynamic characterization

Chen, J.Zhang, L.Zhang, Y.Zhang, H.Du, J.Ding, J.Guo, Y.Jiang, H.Shen, X.

(2009) BMC Microbiol 9: 91-91

  • DOI: https://doi.org/10.1186/1471-2180-9-91
  • Primary Citation of Related Structures:  
    3ED0

  • PubMed Abstract: 

    The natural product Emodin demonstrates a wide range of pharmacological properties including anticancer, anti-inflammatory, antiproliferation, vasorelaxant and anti-H. pylori activities. Although its H. pylori inhibition was discovered, no acting target information against Emodin has been revealed to date. Here we reported that Emodin functioned as a competitive inhibitor against the recombinant beta-hydroxyacyl-ACP dehydratase from Helicobacter pylori (HpFabZ), and strongly inhibited the growth of H. pylori strains SS1 and ATCC 43504. Surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) based assays have suggested the kinetic and thermodynamic features of Emodin/HpFabZ interaction. Additionally, to inspect the binding characters of Emodin against HpFabZ at atomic level, the crystal structure of HpFabZ-Emodin complex was also examined. The results showed that Emodin inhibition against HpFabZ could be implemented either through its occupying the entrance of the tunnel or embedding into the tunnel to prevent the substrate from accessing the active site. Our work is expected to provide useful information for illumination of Emodin inhibition mechanism against HpFabZ, while Emodin itself could be used as a potential lead compound for further anti-bacterial drug discovery.


  • Organizational Affiliation

    Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China. jingchen@mail.shcnc.ac.cn


Macromolecules
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 (PDB Primary Data), 4.2.1.59 (UniProt)
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EMO
Query on EMO

Download Ideal Coordinates CCD File 
J [auth A],
O [auth C]
3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE
C15 H10 O5
RHMXXJGYXNZAPX-UHFFFAOYSA-N
BEN
Query on BEN

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth B]
L [auth B]
P [auth D]
G [auth A],
H [auth A],
K [auth B],
L [auth B],
P [auth D],
R [auth E],
S [auth E]
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A]
M [auth B]
N [auth C]
Q [auth D]
T [auth E]
I [auth A],
M [auth B],
N [auth C],
Q [auth D],
T [auth E],
U [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
EMO PDBBind:  3ED0 Kd: 450 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.204α = 90
b = 100.397β = 90
c = 186.431γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
SCALAdata scaling
CNSrefinement
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    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