4P8M

Crystal structure of M. tuberculosis DprE1 in complex with the non-covalent inhibitor QN114


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

2-Carboxyquinoxalines Kill Mycobacterium tuberculosis through Noncovalent Inhibition of DprE1.

Neres, J.Hartkoorn, R.C.Chiarelli, L.R.Gadupudi, R.Pasca, M.R.Mori, G.Venturelli, A.Savina, S.Makarov, V.Kolly, G.S.Molteni, E.Binda, C.Dhar, N.Ferrari, S.Brodin, P.Delorme, V.Landry, V.de Jesus Lopes Ribeiro, A.L.Farina, D.Saxena, P.Pojer, F.Carta, A.Luciani, R.Porta, A.Zanoni, G.De Rossi, E.Costi, M.P.Riccardi, G.Cole, S.T.

(2015) Acs Chem.Biol. 10: 705-714

  • DOI: 10.1021/cb5007163
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phenotypic screening of a quinoxaline library against replicating Mycobacterium tuberculosis led to the identification of lead compound Ty38c (3-((4-methoxybenzyl)amino)-6-(trifluoromethyl)quinoxaline-2-carboxylic acid). With an MIC99 and MBC of 3.1 ...

    Phenotypic screening of a quinoxaline library against replicating Mycobacterium tuberculosis led to the identification of lead compound Ty38c (3-((4-methoxybenzyl)amino)-6-(trifluoromethyl)quinoxaline-2-carboxylic acid). With an MIC99 and MBC of 3.1 μM, Ty38c is bactericidal and active against intracellular bacteria. To investigate its mechanism of action, we isolated mutants resistant to Ty38c and sequenced their genomes. Mutations were found in rv3405c, coding for the transcriptional repressor of the divergently expressed rv3406 gene. Biochemical studies clearly showed that Rv3406 decarboxylates Ty38c into its inactive keto metabolite. The actual target was then identified by isolating Ty38c-resistant mutants of an M. tuberculosis strain lacking rv3406. Here, mutations were found in dprE1, encoding the decaprenylphosphoryl-d-ribose oxidase DprE1, essential for biogenesis of the mycobacterial cell wall. Genetics, biochemical validation, and X-ray crystallography revealed Ty38c to be a noncovalent, noncompetitive DprE1 inhibitor. Structure-activity relationship studies generated a family of DprE1 inhibitors with a range of IC50's and bactericidal activity. Co-crystal structures of DprE1 in complex with eight different quinoxaline analogs provided a high-resolution interaction map of the active site of this extremely vulnerable target in M. tuberculosis.


    Organizational Affiliation

    †More Medicines for Tuberculosis (MM4TB) Consortium (www.mm4tb.org).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable decaprenylphosphoryl-beta-D-ribose oxidase
A, B
480Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Gene Names: dprE1
EC: 1.1.98.3
Find proteins for P9WJF1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WJF1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
R58
Query on R58

Download SDF File 
Download CCD File 
A, B
3-[(4-ethoxybenzyl)amino]-6-(trifluoromethyl)quinoxaline-2-carboxylic acid
C19 H16 F3 N3 O3
GGCSQMNZKHRBJW-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
2J3
Query on 2J3

Download SDF File 
Download CCD File 
A
(2R)-2-{[(2R)-2-{[(2R)-2-hydroxypropyl]oxy}propyl]oxy}propan-1-ol
C9 H20 O4
LCZVSXRMYJUNFX-IWSPIJDZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
R58IC50: 88 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.243α = 90.00
b = 83.981β = 100.53
c = 90.052γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
European CommissionSwitzerland260872

Revision History 

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-02-04
    Type: Derived calculations
  • Version 1.2: 2015-04-01
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Derived calculations, Other, Refinement description, Source and taxonomy