2VVT

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

• PDB DOI: https://doi.org/10.2210/pdb2VVT/pdb

• Classification: ISOMERASE
• Organism(s): Enterococcus faecalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-11 Released: 2008-06-24 
• Deposition Author(s): Geng, B., Breault, G., Comita-Prevoir, J., Petrichko, R., Eyermann, C., Lundqvist, T., Doig, P., Gorseth, E., Noonan, B.

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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 

Starting Model: experimental

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

• PubMed: 18614367 
• DOI: https://doi.org/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.

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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 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 63.68 kDa 
• Atom Count: 4,836 
• Modelled Residue Count: 536 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE RACEMASE	A, B	290	Enterococcus faecalis	Mutation(s): 0  EC: 5.1.1.3
UniProt
Find proteins for Q836J0 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q836J0  Go to UniProtKB:  Q836J0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I24	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
DGL	D [auth A], F [auth B]	D-GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-GSVOUGTGSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
I24	BindingDB:  2VVT	IC50: 5800 (nM) from 1 assay(s)
	PDBBind:  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 = 44.402	α = 90
b = 69.432	β = 90
c = 165.12	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: 2008-06-24 
Deposition Author(s): Geng, B., Breault, G., Comita-Prevoir, J., Petrichko, R., Eyermann, C., Lundqvist, T., Doig, P., Gorseth, E., Noonan, B.

Revision History  

• 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
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description