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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 3.0 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: https://doi.org/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, 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor Tu 1394Escherichia coli K-12Mutation(s): 0 
Gene Names: tufAb3339JW3301
UniProt
Find proteins for P0CE47 (Escherichia coli (strain K12))
Explore P0CE47 
Go to UniProtKB:  P0CE47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CE47
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Thiocillin GE2270 analogue NVP-LFF57112Planobispora roseaMutation(s): 0 
UniProt
Find proteins for Q7M0J8 (Planobispora rosea)
Explore Q7M0J8 
Go to UniProtKB:  Q7M0J8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7M0J8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
C [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  6 Unique
IDChains TypeFormula2D DiagramParent
BB6
Query on BB6
B
PEPTIDE LINKINGC4 H7 N O2 SCYS
BB7
Query on BB7
B
PEPTIDE LINKINGC5 H9 N O3 SCYS
BB8
Query on BB8
B
L-PEPTIDE LINKINGC9 H11 N O3PHE
BB9
Query on BB9
B
PEPTIDE LINKINGC3 H5 N O2 SCYS
MEN
Query on MEN
B
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
MH6
Query on MH6
B
PEPTIDE LINKINGC3 H5 N O3SER
Biologically Interesting Molecules (External Reference) 1 Unique
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



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2012-12-12
    Changes: Other
  • Version 2.0: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Structure summary
  • Version 3.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations