2XPC

Second-generation sulfonamide inhibitors of MurD: Activity optimisation with conformationally rigid analogues of D-glutamic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Second-Generation Sulfonamide Inhibitors of D- Glutamic Acid-Adding Enzyme: Activity Optimisation with Conformationally Rigid Analogues of D- Glutamic Acid.

Sosi, I.Barreteau, H.Sim, M.Sink, R.Cesar, J.Zega, A.Grdadolnik, S.G.Contreras-Martel, C.Dessen, A.Amoroso, A.Joris, B.Blanot, D.Gobec, S.

(2011) Eur J Med Chem 46: 2880

  • DOI: https://doi.org/10.1016/j.ejmech.2011.04.011
  • Primary Citation of Related Structures:  
    2XPC

  • PubMed Abstract: 

    D-Glutamic acid-adding enzyme (MurD) catalyses the essential addition of d-glutamic acid to the cytoplasmic peptidoglycan precursor UDP-N-acetylmuramoyl-l-alanine, and as such it represents an important antibacterial drug-discovery target enzyme. Based on a series of naphthalene-N-sulfonyl-d-Glu derivatives synthesised recently, we synthesised two series of new, optimised sulfonamide inhibitors of MurD that incorporate rigidified mimetics of d-Glu. The compounds that contained either constrained d-Glu or related rigid d-Glu mimetics showed significantly better inhibitory activities than the parent compounds, thereby confirming the advantage of molecular rigidisation in the design of MurD inhibitors. The binding modes of the best inhibitors were examined with high-resolution NMR spectroscopy and X-ray crystallography. We have solved a new crystal structure of the complex of MurD with an inhibitor bearing a 4-aminocyclohexane-1,3-dicarboxyl moiety. These data provide an additional step towards the development of sulfonamide inhibitors with potential antibacterial activities.


  • Organizational Affiliation

    Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE439Escherichia coliMutation(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
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
051
Query on 051

Download Ideal Coordinates CCD File 
B [auth A](1R,3R,4S)-4-[({6-[(4-CYANO-2-FLUOROBENZYL)OXY]NAPHTHALEN-2-YL}SULFONYL)AMINO]CYCLOHEXANE-1,3-DICARBOXYLIC ACID
C26 H23 F N2 O7 S
NYXJFBFDAFPUOG-XANCMCCPSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [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]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.659α = 90
b = 65.659β = 90
c = 135.642γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-18
    Type: Initial release
  • Version 1.1: 2011-08-10
    Changes: Database references, Version format compliance
  • Version 1.2: 2018-02-07
    Changes: Source and taxonomy
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description