3U2Q

EF-Tu (Escherichia coli) in complex with NVP-LFF571


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of LFF571: an investigational agent for Clostridium difficile infection.

LaMarche, M.J.Leeds, J.A.Amaral, A.Brewer, J.T.Bushell, S.M.Deng, G.Dewhurst, J.M.Ding, J.Dzink-Fox, J.Gamber, G.Jain, A.Lee, K.Lee, L.Lister, T.McKenney, D.Mullin, S.Osborne, C.Palestrant, D.Patane, M.A.Rann, E.M.Sachdeva, M.Shao, J.Tiamfook, S.Trzasko, A.Whitehead, L.Yifru, A.Yu, D.Yan, W.Zhu, Q.

(2012) J.Med.Chem. 55: 2376-2387

  • DOI: 10.1021/jm201685h

  • PubMed Abstract: 
  • Clostridium difficile (C. difficile) is a Gram positive, anaerobic bacterium that infects the lumen of the large intestine and produces toxins. This results in a range of syndromes from mild diarrhea to severe toxic megacolon and death. Alarmingly, t ...

    Clostridium difficile (C. difficile) is a Gram positive, anaerobic bacterium that infects the lumen of the large intestine and produces toxins. This results in a range of syndromes from mild diarrhea to severe toxic megacolon and death. Alarmingly, the prevalence and severity of C. difficile infection are increasing; thus, associated morbidity and mortality rates are rising. 4-Aminothiazolyl analogues of the antibiotic natural product GE2270 A (1) were designed, synthesized, and optimized for the treatment of C. difficile infection. The medicinal chemistry effort focused on enhancing aqueous solubility relative to that of the natural product and previous development candidates (2, 3) and improving antibacterial activity. Structure-activity relationships, cocrystallographic interactions, pharmacokinetics, and efficacy in animal models of infection were characterized. These studies identified a series of dicarboxylic acid derivatives, which enhanced solubility/efficacy profile by several orders of magnitude compared to previously studied compounds and led to the selection of LFF571 (4) as an investigational new drug for treating C. difficile infection.


    Organizational Affiliation

    Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA. matthew.lamarche@novartis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Elongation factor Tu 1
A
394Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: tufA
Find proteins for P0CE47 (Escherichia coli (strain K12))
Go to UniProtKB:  P0CE47
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Thiocillin GE2270 analogue NVP-LFF571
B
12Planobispora roseaMutation(s): 0 
Find proteins for Q7M0J8 (Planobispora rosea)
Go to UniProtKB:  Q7M0J8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001072
Query on PRD_001072
BThiocillin GE2270 analogue NVP-LFF571Thiopeptide / Antibiotic

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.233 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 83.303α = 90.00
b = 132.473β = 90.00
c = 37.433γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-10-04 
  • Released Date: 2012-05-02 
  • Deposition Author(s): Palestrant, D.J.

Revision History 

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Other