4M52

Structure of Mtb Lpd bound to SL827


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Lipoamide channel-binding sulfonamides selectively inhibit mycobacterial lipoamide dehydrogenase.

Bryk, R.Arango, N.Maksymiuk, C.Balakrishnan, A.Wu, Y.T.Wong, C.H.Masquelin, T.Hipskind, P.Lima, C.D.Nathan, C.

(2013) Biochemistry 52: 9375-9384

  • DOI: https://doi.org/10.1021/bi401077f
  • Primary Citation of Related Structures:  
    4M52

  • PubMed Abstract: 

    Tuberculosis remains a global health emergency that calls for treatment regimens directed at new targets. Here we explored lipoamide dehydrogenase (Lpd), a metabolic and detoxifying enzyme in Mycobacterium tuberculosis (Mtb) whose deletion drastically impairs Mtb's ability to establish infection in the mouse. Upon screening more than 1.6 million compounds, we identified N-methylpyridine 3-sulfonamides as potent and species-selective inhibitors of Mtb Lpd affording >1000-fold selectivity versus the human homologue. The sulfonamides demonstrated low nanomolar affinity and bound at the lipoamide channel in an Lpd-inhibitor cocrystal. Their selectivity could be attributed, at least partially, to hydrogen bonding of the sulfonamide amide oxygen with the species variant Arg93 in the lipoamide channel. Although potent and selective, the sulfonamides did not enter mycobacteria, as determined by their inability to accumulate in Mtb to effective levels or to produce changes in intracellular metabolites. This work demonstrates that high potency and selectivity can be achieved at the lipoamide-binding site of Mtb Lpd, a site different from the NAD⁺/NADH pocket targeted by previously reported species-selective triazaspirodimethoxybenzoyl inhibitors.


  • Organizational Affiliation

    Department of Microbiology and Immunology and ‡Department of Pharmacology, Weill Cornell Medical College , New York, New York 10065, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrolipoyl dehydrogenase
A, B, C, D
466Mycobacterium tuberculosisMutation(s): 0 
Gene Names: lpdLPD RV0462lpdCMT0478MTV038.06Rv0462
EC: 1.8.1.4
UniProt
Find proteins for P9WHH9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHH9 
Go to UniProtKB:  P9WHH9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WHH9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
M52 BindingDB:  4M52 Ki: 140 (nM) from 1 assay(s)
IC50: 960 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.521α = 90
b = 111.953β = 94.43
c = 98.034γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2013-11-27 
  • Deposition Author(s): Lima, C.D.

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-27
    Type: Initial release
  • Version 1.1: 2013-12-18
    Changes: Database references
  • Version 1.2: 2014-01-15
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description