5JO0

Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC56 and manganese


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    5JNL, 5JO0, 5JBI, 5JAZ, 5JC1, 5JMP, 5JMW

  • 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-hydroxyacetamido)propyl)phosphonic acid, 2] potently inhibit 1-deoxy-d-xylulose-5-phosphate reductoisomerase (Dxr), a key enzyme in this biosynthetic pathway ...

    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. sherry.mowbray@icm.uu.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplasticA, B422Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: DXRPF14_0641
EC: 1.1.1.267
UniProt
Find proteins for Q8IKG4 (Plasmodium falciparum (isolate 3D7))
Explore Q8IKG4 
Go to UniProtKB:  Q8IKG4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L56 (Subject of Investigation/LOI)
Query on L56

Download Ideal Coordinates CCD File 
C [auth A], L [auth B][(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(3-methylphenyl)pentyl]phosphonic acid
C15 H24 N O5 P
LKGTWQXFDFYGBW-CQSZACIVSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A], N [auth B], O [auth B], P [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
6LR
Query on 6LR

Download Ideal Coordinates CCD File 
K [auth A]morpholine
C4 H9 N O
YNAVUWVOSKDBBP-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], Q [auth B], R [auth B], S [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
D [auth A], M [auth B]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
L56 Binding MOAD:  5JO0 IC50: 50 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.755α = 103.44
b = 55.951β = 103.03
c = 85.619γ = 100.49
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
Omodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FORMASSweden--
VRSweden--

Revision History  (Full details and data files)

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