4MQY

Crystal Structure of the Escherichia coli LpxC/LPC-138 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural Basis of the Promiscuous Inhibitor Susceptibility of Escherichia coli LpxC.

Lee, C.J.Liang, X.Gopalaswamy, R.Najeeb, J.Ark, E.D.Toone, E.J.Zhou, P.

(2014) ACS Chem Biol 9: 237-246

  • DOI: 10.1021/cb400067g
  • Primary Citation of Related Structures:  
    4IS9, 4ISA, 4MQY

  • PubMed Abstract: 
  • The LpxC enzyme in the lipid A biosynthetic pathway is one of the most promising and clinically unexploited antibiotic targets for treatment of multidrug-resistant Gram-negative infections. Progress in medicinal chemistry has led to the discovery of potent LpxC inhibitors with a variety of chemical scaffolds and distinct antibiotic profiles ...

    The LpxC enzyme in the lipid A biosynthetic pathway is one of the most promising and clinically unexploited antibiotic targets for treatment of multidrug-resistant Gram-negative infections. Progress in medicinal chemistry has led to the discovery of potent LpxC inhibitors with a variety of chemical scaffolds and distinct antibiotic profiles. The vast majority of these compounds, including the nanomolar inhibitors L-161,240 and BB-78485, are highly effective in suppressing the activity of Escherichia coli LpxC (EcLpxC) but not divergent orthologs such as Pseudomonas aeruginosa LpxC (PaLpxC) in vitro. The molecular basis for such promiscuous inhibition of EcLpxC has remained poorly understood. Here, we report the crystal structure of EcLpxC bound to L-161,240, providing the first molecular insight into L-161,240 inhibition. Additionally, structural analysis of the EcLpxC/L-161,240 complex together with the EcLpxC/BB-78485 complex reveals an unexpected backbone flipping of the Insert I βa-βb loop in EcLpxC in comparison with previously reported crystal structures of EcLpxC complexes with l-threonyl-hydroxamate-based broad-spectrum inhibitors. Such a conformational switch, which has only been observed in EcLpxC but not in divergent orthologs such as PaLpxC, results in expansion of the active site of EcLpxC, enabling it to accommodate LpxC inhibitors with a variety of head groups, including compounds containing single (R- or S-enantiomers) or double substitutions at the neighboring Cα atom of the hydroxamate warhead group. These results highlight the importance of understanding inherent conformational plasticity of target proteins in lead optimization.


    Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylaseA305Escherichia coliMutation(s): 0 
Gene Names: ECOK1_0097envAlpxC
EC: 3.5.1 (PDB Primary Data), 3.5.1.108 (UniProt)
UniProt
Find proteins for P0A725 (Escherichia coli (strain K12))
Explore P0A725 
Go to UniProtKB:  P0A725
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A725
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2CW
Query on 2CW

Download Ideal Coordinates CCD File 
C [auth A]4-[4-(4-aminophenyl)buta-1,3-diyn-1-yl]-N-[(2S,3R)-3-hydroxy-2-methyl-1-nitroso-1-oxobutan-2-yl]benzamide
C22 H19 N3 O4
TVYJPPDJMQUKRB-QRQCRPRQSA-N
 Ligand Interaction
UKW
Query on UKW

Download Ideal Coordinates CCD File 
J [auth A]4-ethynyl-N-[(1S,2R)-2-hydroxy-1-(oxocarbamoyl)propyl]benzamide
C13 H12 N2 O4
JJXZDQZGPLQGCP-KCJUWKMLSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download Ideal Coordinates CCD File 
D [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.515α = 90
b = 107.515β = 90
c = 53.603γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2014-02-12
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description