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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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

  • 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 p ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTAMATE RACEMASE
A, B, E, F
255Helicobacter pylori (strain J99 / ATCC 700824)Mutation(s): 0 
Gene Names: murI (glr)
EC: 5.1.1.3
Find proteins for Q9ZLT0 (Helicobacter pylori (strain J99 / ATCC 700824))
Go to UniProtKB:  Q9ZLT0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VGA
Query on VGA

Download SDF File 
Download CCD File 
B, 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 SDF File 
Download CCD File 
A, B, E, F
D-GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-GSVOUGTGSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VGAIC50: 500 nM (100) BINDINGDB
DGLKi: 5800 nM (93) BINDINGDB
VGAIC50: 500 nM BINDINGMOAD
VGAIC50: 500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.074α = 90.00
b = 93.982β = 91.46
c = 101.295γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-11-25 
  • 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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-08-09
    Type: Data collection, Database references