3ZI0

Structure of Mycobacterium tuberculosis DXR in complex with a fosmidomycin analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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: 
    • 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 D Biol Crystallogr 62: 807
    • 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
    • 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
    • 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 D Biol Crystallogr 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 TUBERCULOSISMutation(s): 0 
Gene Names: dxrRv2870cMTCY274.01c
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
FM8
Query on FM8

Download CCD File 
A
[(1S)-1-(3,4-dichlorophenyl)-3-{hydroxy[2-(1H-1,2,4-triazol-1-ylmethyl)benzoyl]amino}propyl]phosphonic acid
C19 H19 Cl2 N4 O5 P
CGKYBZFXVQNZBL-SFHVURJKSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FM8Kd:  40   nM  BindingDB
FM8IC50:  13000   nM  BindingDB
FM8IC50:  13000   nM  Binding MOAD
FM8Kd:  40   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.447α = 90
b = 68.707β = 107.34
c = 85.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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