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

  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1016/j.chembiol.2012.09.018
  • Primary Citation of Related Structures:  
    3S9I, 3S9Z, 3SAD, 3SAZ, 3SB0

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malate synthase G741Mycobacterium tuberculosisMutation(s): 1 
Gene Names: glcBGlcB (Rv1837c)MT1885MTCY1A11.06Rv1837c
Find proteins for P9WK17 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WK17 
Go to UniProtKB:  P9WK17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WK17
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
I93 BindingDB:  3SB0 IC50: 5500 (nM) from 1 assay(s)
PDBBind:  3SB0 IC50: 5500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.534α = 90
b = 78.534β = 90
c = 224.07γ = 90
Software Package:
Software NamePurpose
PHENIXmodel building
HKL-3000data reduction
HKL-3000data scaling
HKL-3000data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2013-02-20
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description