2Y1O

Dual-target Inhibitor of MurD and MurE Ligases: Design, Synthesis and Binding Mode Studies


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Dual Inhibitor of MurD and MurE Ligases from Escherichia coli and Staphylococcus aureus.

Tomasic, T.Sink, R.Zidar, N.Fic, A.Contreras-Martel, C.Dessen, A.Patin, D.Blanot, D.Muller-Premru, M.Gobec, S.Zega, A.Kikelj, D.Masic, L.P.

(2012) ACS Med Chem Lett 3: 626-630

  • DOI: https://doi.org/10.1021/ml300047h
  • Primary Citation of Related Structures:  
    2Y1O

  • PubMed Abstract: 

    MurD and MurE ligases, consecutive enzymes participating in the intracellular steps of bacterial peptidoglycan biosynthesis, are important targets for antibacterial drug discovery. We have designed, synthesized, and evaluated the first d-glutamic acid-containing dual inhibitor of MurD and MurE ligases from Escherichia coli and Staphylococcus aureus (IC50 values between 6.4 and 180 μM) possessing antibacterial activity against Gram-positive S. aureus and its methicillin-resistant strain (MRSA) with minimal inhibitory concentration (MIC) values of 8 μg/mL. The inhibitor was also found to be noncytotoxic for human HepG2 cells at concentrations below 200 μM.


  • Organizational Affiliation

    Institut de Biologie Structurale, Bacterial Pathogenesis Group, Université Grenoble I , 38027 Grenoble, France ; Commissariat à l'Energie Atomique (CEA) , IBS, 38027 Grenoble, France ; Centre National de la Recherche Scientifique (CNRS) , IBS, 41 rue Jules Horowitz, 38027 Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE445Escherichia coli DH5[alpha]Mutation(s): 0 
EC: 6.3.2.9
UniProt
Find proteins for P14900 (Escherichia coli (strain K12))
Explore P14900 
Go to UniProtKB:  P14900
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14900
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T26
Query on T26

Download Ideal Coordinates CCD File 
B [auth A](2R)-2-[[3-[[4-[(Z)-(4-OXO-2-SULFANYLIDENE-1,3-THIAZOLIDIN-5-YLIDENE)METHYL]PHENYL]METHYLAMINO]PHENYL]CARBONYLAMINO]PENTANEDIOIC ACID
C23 H21 N3 O6 S2
ZDOPULPHJIBVJX-RMFUMNGISA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Binding Affinity Annotations 
IDSourceBinding Affinity
T26 PDBBind:  2Y1O IC50: 8200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.844α = 90
b = 65.844β = 90
c = 135.747γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Database references
  • Version 1.2: 2017-12-20
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description