2Y1O | pdb_00002y1o

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

• PDB DOI: https://doi.org/10.2210/pdb2Y1O/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli DH5[alpha]
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): No 


• Deposited: 2010-12-09 Released: 2011-12-28 
• Deposition Author(s): Tomasic, T., Sink, R., Kovac, A., Turk, S., Contreras-Martel, C., Dessen, A., Blanot, D., Gobec, S., Zega, A., Kikelj, D., Peterlin-Masic, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

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

• PubMed: 24900523 
• DOI: https://doi.org/10.1021/ml300047h
• Primary Citation 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.

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Organizational Affiliation: 
• Faculty of Pharmacy, University of Ljubljana , Aškerčeva 7, 1000 Ljubljana, Slovenia.
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.
Univ Paris-Sud , Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619, 91405 Orsay, France ; CNRS , 91405 Orsay, France.
Institute of Microbiology and Immunology, Medical Faculty, University of Ljubljana , 1105 Ljubljana, Slovenia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.18 kDa 
• Atom Count: 3,835 
• Modeled Residue Count: 435 
• Deposited Residue Count: 445 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE	A	445	Escherichia 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T26	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	G [auth A], H [auth A], I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	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
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.844	α = 90
b = 65.844	β = 90
c = 135.747	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-28 
Deposition Author(s): Tomasic, T., Sink, R., Kovac, A., Turk, S., Contreras-Martel, C., Dessen, A., Blanot, D., Gobec, S., Zega, A., Kikelj, D., Peterlin-Masic, L.

Revision History  

• 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