3U2Q

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 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
  • Primary Citation of Related Structures:  
    3U2Q

  • 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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor Tu 1A394Escherichia coli K-12Mutation(s): 0 
Gene Names: tufA, b3339, JW3301
Find proteins for P0CE47 (Escherichia coli (strain K12))
Explore P0CE47 
Go to UniProtKB:  P0CE47
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Thiocillin GE2270 analogue NVP-LFF571B12N/AMutation(s): 0 
Find proteins for Q7M0J8 (Planobispora rosea)
Explore Q7M0J8 
Go to UniProtKB:  Q7M0J8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download Ideal Coordinates CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
BB6
Query on BB6		BPEPTIDE LINKINGC4 H7 N O2 SCYS
BB7
Query on BB7		BPEPTIDE LINKINGC5 H9 N O3 SCYS
BB8
Query on BB8		BL-PEPTIDE LINKINGC9 H11 N O3PHE
BB9
Query on BB9		BPEPTIDE LINKINGC3 H5 N O2 SCYS
MEN
Query on MEN		BL-PEPTIDE LINKINGC5 H10 N2 O3ASN
MH6
Query on MH6		BPEPTIDE LINKINGC3 H5 N O3SER
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001072
Query on PRD_001072		BThiocillin GE2270 analogue NVP-LFF571Thiopeptide /  Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 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
b = 132.473β = 90
c = 37.433γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

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
    Changes: Other