3DP0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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:  
    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 ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
(3R)-hydroxymyristoyl-acyl carrier protein dehydratase
A, B, C, D, E, F
A, B, C, D, E, F
159Helicobacter pyloriMutation(s): 0 
Gene Names: fabZBB395_03990BFR58_03630DD756_07280DD767_06730DDP42_00065EC592_05795EDA73_06725HPPMSS1_c00137
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2BC
Query on 2BC

Download Ideal Coordinates CCD File 
K [auth B]N'-[(1E)-(3,5-dibromo-2,4-dihydroxyphenyl)methylidene]naphthalene-2-carbohydrazide
C18 H12 Br2 N2 O3
LVLHTGJPIBVDTM-ZVBGSRNCSA-N
 Ligand Interaction
BEN
Query on BEN

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B],
M [auth C],
P [auth E],
Q [auth E],
H [auth A],
J [auth B],
M [auth C],
P [auth E],
Q [auth E],
R [auth E],
S [auth E]
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
L [auth C],
N [auth D],
O [auth E],
G [auth A],
I [auth B],
L [auth C],
N [auth D],
O [auth E],
T [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
2BC PDBBind:  3DP0 IC50: 1420 (nM) from 1 assay(s)
Binding MOAD:  3DP0 IC50: 1420 (nM) from 1 assay(s)
BindingDB:  3DP0 IC50: 1420 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.07α = 90
b = 100.55β = 90
c = 186.487γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
SCALAdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CrystalCleardata 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: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance