2W4I

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

• PDB DOI: https://doi.org/10.2210/pdb2W4I/pdb

• Classification: ISOMERASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-25 Released: 2008-12-09 
• Deposition Author(s): Lundqvist, T.

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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

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

• PubMed: 19097892 
• 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.

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Organizational Affiliation: 

AstraZeneca R&D Boston, Infection Discovery, 35 Gatehouse Drive, Waltham, MA 02451, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 115.46 kDa 
• Atom Count: 9,466 
• Modelled Residue Count: 1,017 
• Deposited Residue Count: 1,020 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE RACEMASE	A, B, C [auth E], D [auth F]	255	Helicobacter pylori	Mutation(s): 0  EC: 5.1.1.3
UniProt
Find proteins for Q9ZLT0 (Helicobacter pylori (strain J99 / ATCC 700824)) Explore Q9ZLT0  Go to UniProtKB:  Q9ZLT0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VGA	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
DGL	E [auth A], F [auth B], H [auth E], J [auth F]	D-GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-GSVOUGTGSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 59.074	α = 90
b = 93.982	β = 91.46
c = 101.295	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-09 
Deposition Author(s): Lundqvist, T.

Revision History  

• 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