5JBQ

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 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: https://doi.org/10.1021/acs.jmedchem.6b00726
  • Primary Citation of Related Structures:  
    5JBQ

  • 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- 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor Tu 1394Escherichia coli K-12Mutation(s): 0 
Gene Names: tufA, b3339, JW3301
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
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
THIOMURACIN ANALOG13synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  5 Unique
IDChains TypeFormula2D DiagramParent
05N
Query on 05N
B
L-PEPTIDE LINKINGC6 H11 N O3PRO
BB6
Query on BB6
B
PEPTIDE LINKINGC4 H7 N O2 SCYS
BB9
Query on BB9
B
PEPTIDE LINKINGC3 H5 N O2 SCYS
H14
Query on H14
B
L-PEPTIDE LINKINGC9 H11 N O3PHE
MH6
Query on MH6
B
PEPTIDE LINKINGC3 H5 N O3SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.35α = 90
b = 125.34β = 90
c = 45.4γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Structure summary