2VVT

Glutamate Racemase (MurI) from E. faecalis in complex with a 9-Benzyl Purine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Exploring 9-Benzyl Purines as Inhibitors of Glutamate Racemase (Muri) in Gram-Positive Bacteria.

Geng, B.Breault, G.Comita-Prevoir, J.Petrichko, R.Eyermann, C.Lundqvist, T.Doig, P.Gorseth, E.Noonan, B.

(2008) Bioorg Med Chem Lett 18: 4368

  • DOI: 10.1016/j.bmcl.2008.06.068
  • Primary Citation of Related Structures:  
    2VVT

  • PubMed Abstract: 
  • An early SAR study of a screening hit series has generated a series of 9-benzyl purines as inhibitors of bacterial glutamate racemase (MurI) with micromolar enzyme potency and improved physical properties. X-ray co-crystal EI structures were obtained.


    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, B290Enterococcus faecalisMutation(s): 0 
EC: 5.1.1.3
UniProt
Find proteins for Q836J0 (Enterococcus faecalis (strain ATCC 700802 / V583))
Explore Q836J0 
Go to UniProtKB:  Q836J0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ836J0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I24
Query on I24

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
2-butoxy-9-(2,6-difluorobenzyl)-N-(2-morpholin-4-ylethyl)-9H-purin-6-amine
C22 H28 F2 N6 O2
UGZWPZWADDDTRN-UHFFFAOYSA-N
 Ligand Interaction
DGL
Query on DGL

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
D-GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-GSVOUGTGSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
I24 Binding MOAD:  2VVT IC50: 5800 (nM) from 1 assay(s)
PDBBind:  2VVT IC50: 5800 (nM) from 1 assay(s)
BindingDB:  2VVT IC50: 5800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.402α = 90
b = 69.432β = 90
c = 165.12γ = 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: 2008-06-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance