5JBQ

EF-TU (ESCHERICHIA COLI) IN COMPLEX WITH THIOMURACIN ANALOG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.006 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Antibacterial and Solubility Optimization of Thiomuracin A.

LaMarche, M.J.Leeds, J.A.Brewer, J.Dean, K.Ding, J.Dzink-Fox, J.Gamber, G.Jain, A.Kerrigan, R.Krastel, P.Lee, K.Lombardo, F.McKenney, D.Neckermann, G.Osborne, C.Palestrant, D.Patane, M.A.Rann, E.M.Robinson, Z.Schmitt, E.Stams, T.Tiamfook, S.Yu, D.Whitehead, L.

(2016) J.Med.Chem. 59: 6920-6928

  • DOI: 10.1021/acs.jmedchem.6b00726

  • PubMed Abstract: 
  • Synthetic studies of the antimicrobial secondary metabolite thiomuracin A (1) provided access to analogues in the Northern region (C2-C10). Selective hydrolysis of the C10 amide of lead compound 2 and subsequent derivatization led to novel carbon- an ...

    Synthetic studies of the antimicrobial secondary metabolite thiomuracin A (1) provided access to analogues in the Northern region (C2-C10). Selective hydrolysis of the C10 amide of lead compound 2 and subsequent derivatization led to novel carbon- and nitrogen-linked analogues (e.g., 3) which improved antibacterial potency across a panel of Gram-positive organisms. In addition, congeners with improved physicochemical properties were identified which proved efficacious in murine sepsis and hamster C. difficile models of disease. Optimal efficacy in the hamster model of C. difficile was achieved with compounds that possessed both potent antibacterial activity and high aqueous solubility.


    Organizational Affiliation

    Infectious Disease Area, Novartis Institutes for Biomedical Research , Emeryville, California 94608, United States.




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
THIOMURACIN ANALOG
B
13N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
05N
Query on 05N
B
L-PEPTIDE LINKINGC6 H11 N O3PRO
H14
Query on H14
B
L-PEPTIDE LINKINGC9 H11 N O3PHE
BB9
Query on BB9
B
PEPTIDE LINKINGC3 H5 N O2 SCYS
6RK
Query on 6RK
B
L-peptide linkingC7 H13 N O2

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BB6
Query on BB6
B
PEPTIDE LINKINGC4 H7 N O2 SCYS
MH6
Query on MH6
B
PEPTIDE LINKINGC3 H5 N O3SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.006 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 80.350α = 90.00
b = 125.340β = 90.00
c = 45.400γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
BUSTERrefinement
BUSTERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2016-08-10
    Type: Database references