4GAE

Crystal structure of plasmodium dxr in complex with a pyridine-containing inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Antimalarial and Structural Studies of Pyridine-containing Inhibitors of 1-Deoxyxylulose-5-phosphate Reductoisomerase.

Xue, J.Diao, J.Cai, G.Deng, L.Zheng, B.Yao, Y.Song, Y.

(2013) ACS Med Chem Lett 4: 278-282

  • DOI: 10.1021/ml300419r

  • PubMed Abstract: 
  • 1-Deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) in the non-mevalonate isoprene biosynthesis pathway is a target for developing antimalarial drugs. Fosmidomycin, a potent DXR inhibitor, showed safety as well as efficacy against P. falciparum mal ...

    1-Deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) in the non-mevalonate isoprene biosynthesis pathway is a target for developing antimalarial drugs. Fosmidomycin, a potent DXR inhibitor, showed safety as well as efficacy against P. falciparum malaria in clinical trials. Based on our previous quantitative structure activity relationship (QSAR) and crystallographic studies, several novel pyridine-containing fosmidomycin derivatives were designed, synthesized and found to be highly potent inhibitors of P. falciparum DXR (PfDXR) having Ki values of 1.9 - 13 nM, with the best one being ~11× more active than fosmidomycin. These compounds also potently block the proliferation of multi-drug resistant P. falciparum with EC50 values as low as 170 nM. A 2.3 Å crystal structure of PfDXR in complex with one of the inhibitors is reported, showing the flexible loop of the protein undergoes conformational changes upon ligand binding and a hydrogen bond and favorable hydrophobic interactions between the pyridine group and PfDXR account for the enhanced activity.


    Organizational Affiliation

    Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplast
A, B
426Plasmodium falciparumGene Names: DXR
EC: 1.1.1.267
Find proteins for O96693 (Plasmodium falciparum)
Go to UniProtKB:  O96693
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FOB
Query on FOB

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A, B
[(1R)-3-[acetyl(hydroxy)amino]-1-(pyridin-4-yl)propyl]phosphonic acid
C10 H15 N2 O5 P
AMWIPWYKSYZXGB-SNVBAGLBSA-N
 Ligand Interaction
NDP
Query on NDP

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A, B
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
FOQ
Query on FOQ

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A, B
[(1S)-3-[acetyl(hydroxy)amino]-1-(pyridin-4-yl)propyl]phosphonic acid
C10 H15 N2 O5 P
AMWIPWYKSYZXGB-JTQLQIEISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FOQKi: 13 nM BINDINGMOAD
FOBKi: 13 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.360α = 90.00
b = 77.280β = 91.50
c = 109.410γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
StructureStudiodata collection
PHASERphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2013-07-10
    Type: Database references