4Y67

Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, RC176, and manganese


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Synthesis and Bioactivity of beta-Substituted Fosmidomycin Analogues Targeting 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase.

Chofor, R.Sooriyaarachchi, S.Risseeuw, M.D.Bergfors, T.Pouyez, J.Johny, C.Haymond, A.Everaert, A.Dowd, C.S.Maes, L.Coenye, T.Alex, A.Couch, R.D.Jones, T.A.Wouters, J.Mowbray, S.L.Van Calenbergh, S.

(2015) J.Med.Chem. 58: 2988-3001

  • DOI: 10.1021/jm5014264
  • Primary Citation of Related Structures:  
  • Also Cited By: 5JO0, 5JNL, 5JMW, 5JMP, 5JC1, 5JBI, 5JAZ

  • PubMed Abstract: 
  • Blocking the 2-C-methyl-d-erythrithol-4-phosphate (MEP) pathway for isoprenoid biosynthesis offers interesting prospects for inhibiting Plasmodium or Mycobacterium spp. growth. Fosmidomycin (1) and its homologue FR900098 (2) potently inhibit 1-deoxy- ...

    Blocking the 2-C-methyl-d-erythrithol-4-phosphate (MEP) pathway for isoprenoid biosynthesis offers interesting prospects for inhibiting Plasmodium or Mycobacterium spp. growth. Fosmidomycin (1) and its homologue FR900098 (2) potently inhibit 1-deoxy-d-xylulose-5-phosphate reductoisomerase (Dxr), a key enzyme in this pathway. Here we introduced aryl or aralkyl substituents at the β-position of the hydroxamate analogue of 2. While direct addition of a β-aryl moiety resulted in poor inhibition, longer linkers between the carbon backbone and the phenyl ring were generally associated with better binding to the enzymes. X-ray structures of the parasite Dxr-inhibitor complexes show that the "longer" compounds generate a substantially different flap structure, in which a key tryptophan residue is displaced, and the aromatic group of the ligand lies between the tryptophan and the hydroxamate's methyl group. Although the most promising new Dxr inhibitors lack activity against Escherichia coli and Mycobacterium smegmatis, they proved to be highly potent inhibitors of Plasmodium falciparum in vitro growth.


    Organizational Affiliation

    §Department of Chemistry, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium.,¶Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.,∥Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia 20110, United States.,#Department of Chemistry, George Washington University, Washington, D.C. 20052, United States.,†Laboratory for Medicinal Chemistry (FFW), Universiteit Gent, Ottergemsesteenweg 460, B-9000 Gent, Belgium.,∇Evenor Consulting Ltd., The New Barn, Mill Lane, Eastry, Kent CT13 0JW, United Kingdom.,‡Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden.,⊥Laboratory of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplast
A, B
422Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
Gene Names: DXR
EC: 1.1.1.267
Find proteins for Q8IKG4 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IKG4
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
RC5
Query on RC5

Download SDF File 
Download CCD File 
A, B
[(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-phenylpentyl]phosphonic acid
C14 H22 N O5 P
YKRNADVNYIPUET-CYBMUJFWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RC5IC50: 117 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.177 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 51.570α = 104.11
b = 56.465β = 103.25
c = 86.024γ = 100.16
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
VetenskapsradetSweden--

Revision History 

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2015-04-22
    Type: Database references