4M52

Structure of Mtb Lpd bound to SL827


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1021/bi401077f

  • 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 drasticall ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrolipoyl dehydrogenase
A, B, C, D
466Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: lpdC (lpd)
EC: 1.8.1.4
Find proteins for P9WHH9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHH9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M52
Query on M52

Download SDF File 
Download CCD File 
A, B, C, D
N~2~-[(2-amino-5-bromopyridin-3-yl)sulfonyl]-N-(4-methoxyphenyl)-N~2~-methylglycinamide
C15 H17 Br N4 O4 S
HMNYMNWOUAJOIH-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
M52IC50: 960 nM (100) BINDINGDB
M52Ki: 140 nM (100) BINDINGDB
M52Ki: 140 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.521α = 90.00
b = 111.953β = 94.43
c = 98.034γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
ADSCdata collection
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-08-07 
  • Released Date: 2013-11-27 
  • Deposition Author(s): Lima, C.D.

Revision History 

  • Version 1.0: 2013-11-27
    Type: Initial release
  • Version 1.1: 2013-12-18
    Type: Database references
  • Version 1.2: 2014-01-15
    Type: Database references