2W4I

Crystal structure of Helicobacter pylori glutamate racemase in complex with D-Glutamate and an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Potent and selective inhibitors of Helicobacter pylori glutamate racemase (MurI): pyridodiazepine amines.

Geng, B.Basarab, G.Comita-Prevoir, J.Gowravaram, M.Hill, P.Kiely, A.Loch, J.MacPherson, L.Morningstar, M.Mullen, G.Osimboni, E.Satz, A.Eyermann, C.Lundqvist, T.

(2009) Bioorg Med Chem Lett 19: 930-936

  • DOI: 10.1016/j.bmcl.2008.11.113
  • Primary Citation of Related Structures:  
    2W4I

  • PubMed Abstract: 
  • An SAR study of an HTS screening hit generated a series of pyridodiazepine amines as potent inhibitors of Helicobacter pylori glutamate racemase (MurI) showing highly selective anti-H. pylori activity, marked improved solubility, and reduced plasma protein binding ...

    An SAR study of an HTS screening hit generated a series of pyridodiazepine amines as potent inhibitors of Helicobacter pylori glutamate racemase (MurI) showing highly selective anti-H. pylori activity, marked improved solubility, and reduced plasma protein binding. X-ray co-crystal E-I structures were obtained. These uncompetitive inhibitors bind at the MurI dimer interface.


    Organizational Affiliation

    AstraZeneca R&D Boston, Infection Discovery, 35 Gatehouse Drive, Waltham, MA 02451, USA. bolin.geng@astrazeneca.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUTAMATE RACEMASEA,
B,
C [auth E],
D [auth F]
255Helicobacter pyloriMutation(s): 0 
EC: 5.1.1.3
UniProt
Find proteins for Q9ZLT0 (Helicobacter pylori (strain J99 / ATCC 700824))
Explore Q9ZLT0 
Go to UniProtKB:  Q9ZLT0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZLT0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VGA
Query on VGA

Download Ideal Coordinates CCD File 
G [auth B],
I [auth E]
1-[(3S)-5-PHENYL-3-THIOPHEN-2-YL-3H-1,4-BENZODIAZEPIN-2-YL]AZETIDIN-3-OL
C22 H19 N3 O S
BKSGACYTXOQQNI-OAQYLSRUSA-N
 Ligand Interaction
DGL
Query on DGL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
H [auth E],
J [auth F]
D-GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-GSVOUGTGSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DGL BindingDB:  2W4I Ki: 5800 (nM) from 1 assay(s)
VGA PDBBind:  2W4I IC50: 500 (nM) from 1 assay(s)
Binding MOAD:  2W4I IC50: 500 (nM) from 1 assay(s)
BindingDB:  2W4I IC50: 500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.074α = 90
b = 93.982β = 91.46
c = 101.295γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-09
    Changes: Data collection, Database references
  • Version 1.4: 2020-03-04
    Changes: Derived calculations, Other