3ZHX

Structure of Mycobacterium tuberculosis DXR in complex with a fosmidomycin analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Dxr Inhibition by Potent Mono- and Disubstituted Fosmidomycin Analogues.

Jansson, A.M.Wieckowska, A.Bjorkelid, C.Yahiaoui, S.Sooriyaarachchi, S.Lindh, M.Bergfors, T.Dharavath, S.Desroses, M.Suresh, S.Andaloussi, M.Nikhil, R.Sreevalli, S.Srinivasa, B.R.Larhed, M.Jones, T.A.Karlen, A.Mowbray, S.L.

(2013) J.Med.Chem. 56: 6190

  • DOI: 10.1021/jm4006498
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The antimalarial compound fosmidomycin targets DXR, the enzyme that catalyzes the first committed step in the MEP pathway, producing the essential isoprenoid precursors, isopentenyl diphosphate and dimethylallyl diphosphate. The MEP pathway is used b ...

    The antimalarial compound fosmidomycin targets DXR, the enzyme that catalyzes the first committed step in the MEP pathway, producing the essential isoprenoid precursors, isopentenyl diphosphate and dimethylallyl diphosphate. The MEP pathway is used by a number of pathogens, including Mycobacterium tuberculosis and apicomplexan parasites, and differs from the classical mevalonate pathway that is essential in humans. Using a structure-based approach, we designed a number of analogues of fosmidomycin, including a series that are substituted in both the Cα and the hydroxamate positions. The latter proved to be a stable framework for the design of inhibitors that extend from the polar and cramped (and so not easily druggable) substrate-binding site and can, for the first time, bridge the substrate and cofactor binding sites. A number of these compounds are more potent than fosmidomycin in terms of killing Plasmodium falciparum in an in vitro assay; the best has an IC50 of 40 nM.


    Related Citations: 
    • Design, Synthesis, and X-Ray Crystallographic Studies of Alpha-Aryl Substituted Fosmidomycin Analogues as Inhibitors of Mycobacterium Tuberculosis 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase.
      Andaloussi, M.,Henriksson, L.M.,Wieckowska, A.,Lindh, M.,Bjorkelid, C.,Larsson, A.M.,Suresh, S.,Iyer, H.,Srinivasa, B.R.,Bergfors, T.,Unge, T.,Mowbray, S.L.,Larhed, M.,Jones, T.A.,Karlen, A.
      (2011) J.Med.Chem. 54: 4964
    • Structures of Mycobacterium Tuberculosis 1-Deoxy-D-Xylulose- 5-Phosphate Reductoisomerase Provide New Insights Into Catalysis.
      Henriksson, L.M.,Unge, T.,Carlsson, J.,Aqvist, J.,Mowbray, S.L.,Jones, T.A.
      (2007) J.Biol.Chem. 282: 19905
    • The 1.9 A Resolution Structure of Mycobacterium Tuberculosis 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, a Potential Drug Target.
      Henriksson, L.M.,Bjorkelid, C.,Mowbray, S.L.,Unge, T.
      (2006) Acta Crystallogr.,Sect.D 62: 807
    • Structural Studies on Mycobacterium Tuberculosis Dxr in Complex with the Antibiotic Fr-900098.
      Bjorkelid, C.,Bergfors, T.,Unge, T.,Mowbray, S.L.,Jones, T.A.
      (2012) Acta Crystallogr.,Sect.D 68: 134


    Organizational Affiliation

    Department of Cell and Molecular Biology, Uppsala University , Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE
A, B
397Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: dxr
EC: 1.1.1.267
Find proteins for P9WNS1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WNS1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
FM6
Query on FM6

Download SDF File 
Download CCD File 
A
[(1S)-1-(3,4-dichlorophenyl)-3-[oxidanyl(phenylcarbonyl)amino]propyl]phosphonic acid
[3-[benzoyl(hydroxy)amino]-1-(3,4-dichlorophenyl)propyl]phosphonic acid
C16 H16 Cl2 N O5 P
ZQCVCGYWPNFEAH-HNNXBMFYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FM6Kd: 210 nM (99) BINDINGDB
FM6IC50: 320 nM (99) BINDINGDB
FM6Kd: 210 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.710α = 90.00
b = 66.990β = 107.90
c = 84.610γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-09
    Type: Initial release