Structure of mycobacterial lipoamide dehydrogenase bound to a triazaspirodimethoxybenzoyl inhibitor

Experimental Data Snapshot

  • Resolution: 2.42 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.185 

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Triazaspirodimethoxybenzoyls as selective inhibitors of mycobacterial lipoamide dehydrogenase .

Bryk, R.Arango, N.Venugopal, A.Warren, J.D.Park, Y.H.Patel, M.S.Lima, C.D.Nathan, C.

(2010) Biochemistry 49: 1616-1627

  • DOI: https://doi.org/10.1021/bi9016186
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Mycobacterium tuberculosis (Mtb) remains the leading single cause of death from bacterial infection. Here we explored the possibility of species-selective inhibition of lipoamide dehydrogenase (Lpd), an enzyme central to Mtb's intermediary metabolism and antioxidant defense. High-throughput screening of combinatorial chemical libraries identified triazaspirodimethoxybenzoyls as high-nanomolar inhibitors of Mtb's Lpd that were noncompetitive versus NADH, NAD(+), and lipoamide and >100-fold selective compared to human Lpd. Efficacy required the dimethoxy and dichlorophenyl groups. The structure of an Lpd-inhibitor complex was resolved to 2.42 A by X-ray crystallography, revealing that the inhibitor occupied a pocket adjacent to the Lpd NADH/NAD(+) binding site. The inhibitor did not overlap with the adenosine moiety of NADH/NAD(+) but did overlap with positions predicted to bind the nicotinamide rings in NADH and NAD(+) complexes. The dimethoxy ring occupied a deep pocket adjacent to the FAD flavin ring where it would block coordination of the NADH nicotinamide ring, while the dichlorophenyl group occupied a more exposed pocket predicted to coordinate the NAD(+) nicotinamide. Several residues that are not conserved between the bacterial enzyme and its human homologue were predicted to contribute both to inhibitor binding and to species selectivity, as confirmed for three residues by analysis of the corresponding mutant Mtb Lpd proteins. Thus, nonconservation of residues lining the electron-transfer tunnel in Mtb Lpd can be exploited for development of species-selective Lpd inhibitors.

  • Organizational Affiliation

    Department of Microbiology and Immunology, Weill Cornell Medical College, New York,New York 10065, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrolipoyl dehydrogenase
A, B
466Mycobacterium tuberculosisMutation(s): 0 
Gene Names: lpdlpd Rv0462MT0478MTV038.06Rv0462
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
C27 H33 N9 O15 P2
Query on 3II

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
C32 H34 Cl2 N4 O5
Binding Affinity Annotations 
IDSourceBinding Affinity
3II Binding MOAD:  3II4 Ki: 865 (nM) from 1 assay(s)
BindingDB:  3II4 IC50: min: 650, max: 1.00e+5 (nM) from 7 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.42 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.9α = 90
b = 98.4β = 90
c = 123.8γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2010-01-26 
  • Deposition Author(s): Lima, C.D.

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description