3U6K | pdb_00003u6k

Ef-tu (escherichia coli) in complex with nvp-ldk733


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.298 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GDPClick on this verticalbar to view details

This is version 2.0 of the entry. See complete history


Literature

Antibacterial optimization of 4-aminothiazolyl analogues of the natural product GE2270 A: identification of the cycloalkylcarboxylic acids.

LaMarche, M.J.Leeds, J.A.Amaral, K.Brewer, J.T.Bushell, S.M.Dewhurst, J.M.Dzink-Fox, J.Gangl, E.Goldovitz, J.Jain, A.Mullin, S.Neckermann, G.Osborne, C.Palestrant, D.Patane, M.A.Rann, E.M.Sachdeva, M.Shao, J.Tiamfook, S.Whitehead, L.Yu, D.

(2011) J Med Chem 54: 8099-8109

  • DOI: https://doi.org/10.1021/jm200938f
  • Primary Citation of Related Structures:  
    3U6B, 3U6K

  • PubMed Abstract: 

    4-Aminothiazolyl analogues of the antibiotic natural product GE2270 A (1) were designed, synthesized, and optimized for their activity against Gram positive bacterial infections. Optimization efforts focused on improving the physicochemical properties (e.g., aqueous solubility and chemical stability) of the 4-aminothiazolyl natural product template while improving the in vitro and in vivo antibacterial activity. Structure-activity relationships were defined, and the solubility and efficacy profiles were improved over those of previous analogues and 1. These studies identified novel, potent, soluble, and efficacious elongation factor-Tu inhibitors, which bear cycloalkylcarboxylic acid side chains, and culminated in the selection of development candidates amide 48 and urethane 58.


  • Organizational Affiliation

    Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States. matthew.lamarche@novartis.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor Tu 1
A, B
394Escherichia 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-LDK733
C, D
12Planobispora 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
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  • Reference Sequence
Small Molecules
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.298 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.372α = 90
b = 82.216β = 90
c = 129.9γ = 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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GDPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Structure summary
  • Version 1.2: 2012-12-12
    Changes: Other
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Structure summary