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 

Starting Model: experimental
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This is version 1.5 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: https://doi.org/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. 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. [email protected]


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence 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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DGL BindingDB:  2W4I Ki: 5800 (nM) from 1 assay(s)
VGA BindingDB:  2W4I IC50: 500 (nM) from 1 assay(s)
PDBBind:  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

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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: 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
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Refinement description