X-ray structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis, in complex with a 3,4- dichlorophenyl-substituted FR900098 analogue and manganese.

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

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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.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

  • DOI: https://doi.org/10.1021/jm2000085
  • Primary Citation of Related Structures:  
    2Y1C, 2Y1D, 2Y1E, 2Y1F, 2Y1G

  • PubMed Abstract: 

    The natural antibiotic fosmidomycin acts via inhibition of 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR), an essential enzyme in the non-mevalonate pathway of isoprenoid biosynthesis. Fosmidomycin is active on Mycobacterium tuberculosis DXR (MtDXR), but it lacks antibacterial activity probably because of poor uptake. α-Aryl substituted fosmidomycin analogues have more favorable physicochemical properties and are also more active in inhibiting malaria parasite growth. We have solved crystal structures of MtDXR in complex with 3,4-dichlorophenyl substituted fosmidomycin analogues; these show important differences compared to our previously described forsmidomycin-DXR complex. Our best inhibitor has an IC(50) = 0.15 μM on MtDXR but still lacked activity in a mycobacterial growth assay (MIC > 32 μg/mL). The combined results, however, provide insights into how DXR accommodates the new inhibitors and serve as an excellent starting point for the design of other novel and more potent inhibitors, particularly against pathogens where uptake is less of a problem, such as the malaria parasite.

  • Organizational Affiliation

    Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751 23 Uppsala, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
398Mycobacterium tuberculosis H37RvMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.525α = 90
b = 65.022β = 101.88
c = 86.227γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2011-08-03
    Changes: Database references, Version format compliance
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description