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: 2.20 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 1.2 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, 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 ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Malate synthase GA741Mycobacterium tuberculosisMutation(s): 1 
Gene Names: glcBGlcB (Rv1837c)MT1885MTCY1A11.06Rv1837c
EC: 2.3.3.9
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I93
Query on I93

Download Ideal Coordinates CCD File 
C [auth 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 Ideal Coordinates CCD File 
B [auth A],
D [auth A],
E [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
REFMACrefinement
PHENIXmodel building
BUSTERrefinement
HKL-3000data reduction
HKL-3000data scaling
REFMACphasing
PHENIXphasing
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