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 

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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.

    • 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
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)
Binding MOAD:  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

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Ligand Structure Quality Assessment 


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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