3SAD

Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 4-(2-mehtylphenyl)-2,4-dioxobutanoic acid inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    3S9I, 3S9Z, 3SAZ, 3SB0, 3SAD

  • 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Malate synthase G A741Mycobacterium tuberculosisMutation(s): 1 
Gene Names: glcBRv1837cMT1885MTCY1A11.06
EC: 2.3.3.9
Find proteins for P9WK17 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WK17 
Go to UniProtKB:  P9WK17
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
040
Query on 040

Download Ideal Coordinates CCD File 
A
4-(2-methylphenyl)-2,4-dioxobutanoic acid
C11 H10 O4
AVVYWVLNDGDANA-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
40IC50 :  1100   nM  PDBBind
040IC50:  1100   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.737α = 90
b = 77.737β = 90
c = 221.986γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
PHENIXmodel building
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
PHENIXphasing
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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