3SB0

Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 4-(2-chloro-6-fluoro-3-methylphenyl)-2,4-dioxobutanoic acid inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.199 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-guided discovery of phenyl-diketo acids as potent inhibitors of M. tuberculosis malate synthase.

Krieger, I.V.Freundlich, J.S.Gawandi, V.B.Roberts, J.P.Gawandi, V.B.Sun, Q.Owen, J.L.Fraile, M.T.Huss, S.I.Lavandera, J.L.Ioerger, T.R.Sacchettini, J.C.

(2012) Chem.Biol. 19: 1556-1567

  • DOI: 10.1016/j.chembiol.2012.09.018
  • Primary Citation of Related Structures:  
  • Also Cited By: 6C8P, 6C7B, 6C6O, 6C2X, 6BU1, 6BA7, 6AXB, 6DNP, 6DLJ, 6DL9, 6DKO, 6AU9, 6ASU, 6AS6, 6APZ, 5T8G, 5H8U, 5H8P, 5H8M, 5ECV, 5E9X, 5DX7, 5DRI, 5DRC, 5CJN, 5CJM, 5CEW, 5CCZ, 5CC7, 5CC6, 5CC5, 5CC3, 5CBJ, 5CBI, 5CBB, 5CAH, 5C9X, 5C9W, 5C9U, 5C9T, 5C9R, 5C7V

  • PubMed Abstract: 
  • The glyoxylate shunt plays an important role in fatty acid metabolism and has been shown to be critical to survival of several pathogens involved in chronic infections. For Mycobacterium tuberculosis (Mtb), a strain with a defective glyoxylate shunt ...

    The glyoxylate shunt plays an important role in fatty acid metabolism and has been shown to be critical to survival of several pathogens involved in chronic infections. For Mycobacterium tuberculosis (Mtb), a strain with a defective glyoxylate shunt was previously shown to be unable to establish infection in a mouse model. We report the development of phenyl-diketo acid (PDKA) inhibitors of malate synthase (GlcB), one of two glyoxylate shunt enzymes, using structure-based methods. PDKA inhibitors were active against Mtb grown on acetate, and overexpression of GlcB ameliorated this inhibition. Crystal structures of complexes of GlcB with PDKA inhibitors guided optimization of potency. A selected PDKA compound demonstrated efficacy in a mouse model of tuberculosis. The discovery of these PDKA derivatives provides chemical validation of GlcB as an attractive target for tuberculosis therapeutics.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Malate synthase G
A
741Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 1 
Gene Names: glcB
EC: 2.3.3.9
Find proteins for P9WK17 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WK17
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I93
Query on I93

Download SDF File 
Download CCD File 
A
4-(2-chloro-6-fluoro-3-methylphenyl)-2,4-dioxobutanoic acid
C11 H8 Cl F O4
ZIEFMRIMKUUCBZ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
I93IC50: 5500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.199 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.172 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.534α = 90.00
b = 78.534β = 90.00
c = 224.070γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
PHENIXphasing
REFMACrefinement
HKL-3000data scaling
BUSTERrefinement
HKL-3000data collection
HKL-3000data reduction
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2013-02-20
    Type: Database references