2X5O

Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- thiazolidine-2,4-dione Inhibitors of MurD Ligase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of novel 5-benzylidenerhodanine and 5-benzylidenethiazolidine-2,4-dione inhibitors of MurD ligase.

Zidar, N.Tomasic, T.Sink, R.Rupnik, V.Kovac, A.Turk, S.Patin, D.Blanot, D.Contreras Martel, C.Dessen, A.Muller Premru, M.Zega, A.Gobec, S.Peterlin Masic, L.Kikelj, D.

(2010) J. Med. Chem. 53: 6584-6594

  • DOI: 10.1021/jm100285g
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We have designed, synthesized, and evaluated 5-benzylidenerhodanine- and 5-benzylidenethiazolidine-2,4-dione-based compounds as inhibitors of bacterial enzyme MurD with E. coli IC(50) in the range 45-206 μM. The high-resolution crystal structure of M ...

    We have designed, synthesized, and evaluated 5-benzylidenerhodanine- and 5-benzylidenethiazolidine-2,4-dione-based compounds as inhibitors of bacterial enzyme MurD with E. coli IC(50) in the range 45-206 μM. The high-resolution crystal structure of MurD in complex with (R,Z)-2-(3-[{4-([2,4-dioxothiazolidin-5-ylidene]methyl)phenylamino}methyl)benzamido)pentanedioic acid [(R)-32] revealed details of the binding mode of the inhibitor within the active site and provides a good foundation for structure-based design of a novel generation of MurD inhibitors.


    Organizational Affiliation

    Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
A
439Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: murD
EC: 6.3.2.9
Find proteins for P14900 (Escherichia coli (strain K12))
Go to UniProtKB:  P14900
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SO3
Query on SO3

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Download CCD File 
A
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
AZI
Query on AZI

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Download CCD File 
A
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
VSV
Query on VSV

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Download CCD File 
A
N-({3-[({4-[(Z)-(2,4-DIOXO-1,3-THIAZOLIDIN-5-YLIDENE)METHYL]PHENYL}AMINO)METHYL]PHENYL}CARBONYL)-D-GLUTAMIC ACID
C23 H21 N3 O7 S
YITBSJALJWUAQA-LVSMMTLPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VSVIC50: 85000 nM BINDINGMOAD
VSVIC50: 85000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.185 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 66.091α = 90.00
b = 66.091β = 90.00
c = 135.781γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-08-31
    Type: Database references, Refinement description, Version format compliance
  • Version 1.2: 2018-02-28
    Type: Database references, Source and taxonomy