3U6B

Ef-tu (escherichia coli) in complex with nvp-ldi028


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1021/jm200938f
  • Primary Citation of Related Structures:  

  • 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 propertie ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Elongation factor Tu 1
A, B
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-LDI028
C, D
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, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001074
Query on PRD_001074
C,DThiocillin GE2270 analogue NVP-LDI028Thiopeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.196 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 97.246α = 90.00
b = 100.376β = 90.00
c = 156.483γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
BUSTERrefinement
PHASERphasing
HKL-2000data scaling
CNXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-10-12 
  • Released Date: 2012-02-08 
  • Deposition Author(s): Palestrant, D.J.

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-04-18
    Type: Structure summary
  • Version 1.2: 2012-12-12
    Type: Other