5JNL

Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC54 and manganese


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Targeting an Aromatic Hotspot in Plasmodium falciparum 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase with beta-Arylpropyl Analogues of Fosmidomycin.

Sooriyaarachchi, S.Chofor, R.Risseeuw, M.D.Bergfors, T.Pouyez, J.Dowd, C.S.Maes, L.Wouters, J.Jones, T.A.Van Calenbergh, S.Mowbray, S.L.

(2016) Chemmedchem 11: 2024-2036

  • DOI: 10.1002/cmdc.201600249
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Blocking the 2-C-methyl-d-erythrithol-4-phosphate pathway for isoprenoid biosynthesis offers new ways to inhibit the growth of Plasmodium spp. Fosmidomycin [(3-(N-hydroxyformamido)propyl)phosphonic acid, 1] and its acetyl homologue FR-900098 [(3-(N-h ...

    Blocking the 2-C-methyl-d-erythrithol-4-phosphate pathway for isoprenoid biosynthesis offers new ways to inhibit the growth of Plasmodium spp. Fosmidomycin [(3-(N-hydroxyformamido)propyl)phosphonic acid, 1] and its acetyl homologue FR-900098 [(3-(N-hydroxyacetamido)propyl)phosphonic acid, 2] potently inhibit 1-deoxy-d-xylulose-5-phosphate reductoisomerase (Dxr), a key enzyme in this biosynthetic pathway. Arylpropyl substituents were introduced at the β-position of the hydroxamate analogue of 2 to study changes in lipophilicity, as well as electronic and steric properties. The potency of several new compounds on the P. falciparum enzyme approaches that of 1 and 2. Activities against the enzyme and parasite correlate well, supporting the mode of action. Seven X-ray structures show that all of the new arylpropyl substituents displace a key tryptophan residue of the active-site flap, which had made favorable interactions with 1 and 2. Plasticity of the flap allows substituents to be accommodated in many ways; in most cases, the flap is largely disordered. Compounds can be separated into two classes based on whether the substituent on the aromatic ring is at the meta or para position. Generally, meta-substituted compounds are better inhibitors, and in both classes, smaller size is linked to better potency.


    Related Citations: 
    • 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


    Organizational Affiliation

    Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, 751 24, Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic
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 4 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
L54
Query on L54

Download SDF File 
Download CCD File 
A, B
{(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-[4-(trifluoromethyl)phenyl]pentyl}phosphonic acid
C15 H21 F3 N O5 P
QJHOMBPUEUGKSC-GFCCVEGCSA-N
 Ligand Interaction
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L54IC50: 270 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.178 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 51.473α = 103.10
b = 56.035β = 102.89
c = 86.041γ = 100.90
Software Package:
Software NamePurpose
Omodel building
REFMACrefinement
SCALAdata scaling
XDSdata processing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FORMASSweden--
VRSweden--

Revision History 

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2016-09-28
    Type: Database references