3WQQ

Crystal structure of PfDXR complexed with inhibitor-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Binding Modes of Reverse Fosmidomycin Analogs toward the Antimalarial Target IspC.

Konzuch, S.Umeda, T.Held, J.Hahn, S.Brucher, K.Lienau, C.Behrendt, C.T.Grawert, T.Bacher, A.Illarionov, B.Fischer, M.Mordmuller, B.Tanaka, N.Kurz, T.

(2014) J.Med.Chem. 57: 8827-8838

  • DOI: 10.1021/jm500850y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 1-Deoxy-d-xylulose 5-phosphate reductoisomerase of Plasmodium falciparum (PfIspC, PfDxr), believed to be the rate-limiting enzyme of the nonmevalonate pathway of isoprenoid biosynthesis (MEP pathway), is a clinically validated antimalarial target. Th ...

    1-Deoxy-d-xylulose 5-phosphate reductoisomerase of Plasmodium falciparum (PfIspC, PfDxr), believed to be the rate-limiting enzyme of the nonmevalonate pathway of isoprenoid biosynthesis (MEP pathway), is a clinically validated antimalarial target. The enzyme is efficiently inhibited by the natural product fosmidomycin. To gain new insights into the structure activity relationships of reverse fosmidomycin analogs, several reverse analogs of fosmidomycin were synthesized and biologically evaluated. The 4-methoxyphenyl substituted derivative 2c showed potent inhibition of PfIspC as well as of P. falciparum growth and was more than one order of magnitude more active than fosmidomycin. The binding modes of three new derivatives in complex with PfIspC, reduced nicotinamide adenine dinucleotide phosphate, and Mg(2+) were determined by X-ray structure analysis. Notably, PfIspC selectively binds the S-enantiomers of the study compounds.


    Organizational Affiliation

    Institut für Pharmazeutische und Medizinische Chemie, Heinrich Heine Universität , Universitätsstr. 1, 40225 Düsseldorf, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplast
A, B
488Plasmodium falciparum (isolate HB3)Mutation(s): 0 
Gene Names: DXR
EC: 1.1.1.267
Find proteins for O96693 (Plasmodium falciparum (isolate HB3))
Go to UniProtKB:  O96693
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
IB3
Query on IB3

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Download CCD File 
A, B
[(1S)-4-[hydroxy(methyl)amino]-1-(4-methylphenyl)-4-oxobutyl]phosphonic acid
C12 H18 N O5 P
YBVPWURHYFIQDS-NSHDSACASA-N
 Ligand Interaction
NDP
Query on NDP

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Download CCD File 
A, B
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IB3IC50: 10 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.042α = 90.00
b = 76.260β = 90.82
c = 104.231γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-01-31 
  • Released Date: 2014-11-26 
  • Deposition Author(s): Tanaka, N., Umeda, T.

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release