4IGF

Crystal structure of Plasmodium falciparum FabI complexed with NAD and inhibitor 3-(4-Chloro-2-hydroxyphenoxy)-7-hydroxy-2H-chromen-2-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design, Synthesis, and Biological and Crystallographic Evaluation of Novel Inhibitors of Plasmodium falciparum Enoyl-ACP-reductase (PfFabI)

Belluti, F.Perozzo, R.Lauciello, L.Colizzi, F.Kostrewa, D.Bisi, A.Gobbi, S.Rampa, A.Bolognesi, M.L.Recanatini, M.Brun, R.Scapozza, L.Cavalli, A.

(2013) J.Med.Chem. 56: 7516-7526

  • DOI: 10.1021/jm400637m
  • Primary Citation of Related Structures:  4IGE

  • PubMed Abstract: 
  • Malaria, a disease of worldwide significance, is responsible for over one million deaths annually. The liver-stage of Plasmodium's life cycle is the first, obligatory, but clinically silent step in malaria infection. The P. falciparum type II fatty a ...

    Malaria, a disease of worldwide significance, is responsible for over one million deaths annually. The liver-stage of Plasmodium's life cycle is the first, obligatory, but clinically silent step in malaria infection. The P. falciparum type II fatty acid biosynthesis pathway (PfFAS-II) has been found to be essential for complete liver-stage development and has been regarded as a potential antimalarial target for the development of drugs for malaria prophylaxis and liver-stage eradication. In this paper, new coumarin-based triclosan analogues are reported and their biological profile is explored in terms of inhibitory potency against enzymes of the PfFAS-II pathway. Among the tested compounds, 7 and 8 showed the highest inhibitory potency against Pf enoyl-ACP-reductase (PfFabI), followed by 15 and 3. Finally, we determined the crystal structures of compounds 7 and 11 in complex with PfFabI to identify their mode of binding and to confirm outcomes of docking simulations.


    Organizational Affiliation

    Department of Pharmacy and Biotechnology, University of Bologna , Via Belmeloro 6, I-40126 Bologna, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Enoyl-acyl carrier reductase
A, B
345Plasmodium falciparum (isolate 3D7)Gene Names: PfENR
EC: 1.3.1.9
Find proteins for C6KSZ2 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  C6KSZ2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CHV
Query on CHV

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Download CCD File 
A, B
3-(4-chloro-2-hydroxyphenoxy)-7-hydroxy-2H-chromen-2-one
C15 H9 Cl O5
UBCXCRQXPSAIBV-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CHVIC50: 6000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.153 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 131.556α = 90.00
b = 131.556β = 90.00
c = 82.635γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description