4R5V

Structure of the m1 alanylaminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Two-Pronged Attack: Dual Inhibition of Plasmodium falciparum M1 and M17 Metalloaminopeptidases by a Novel Series of Hydroxamic Acid-Based Inhibitors.

Mistry, S.N.Drinkwater, N.Ruggeri, C.Sivaraman, K.K.Loganathan, S.Fletcher, S.Drag, M.Paiardini, A.Avery, V.M.Scammells, P.J.McGowan, S.

(2014) J.Med.Chem. 57: 9168-9183

  • DOI: 10.1021/jm501323a
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Plasmodium parasites, the causative agents of malaria, have developed resistance to most of our current antimalarial therapies, including artemisinin combination therapies which are widely described as our last line of defense. Antimalarial agents wi ...

    Plasmodium parasites, the causative agents of malaria, have developed resistance to most of our current antimalarial therapies, including artemisinin combination therapies which are widely described as our last line of defense. Antimalarial agents with a novel mode of action are urgently required. Two Plasmodium falciparum aminopeptidases, PfA-M1 and PfA-M17, play crucial roles in the erythrocytic stage of infection and have been validated as potential antimalarial targets. Using compound-bound crystal structures of both enzymes, we have used a structure-guided approach to develop a novel series of inhibitors capable of potent inhibition of both PfA-M1 and PfA-M17 activity and parasite growth in culture. Herein we describe the design, synthesis, and evaluation of a series of hydroxamic acid-based inhibitors and demonstrate the compounds to be exciting new leads for the development of novel antimalarial therapeutics.


    Organizational Affiliation

    Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
M1 family aminopeptidase
A
895Plasmodium falciparum (isolate FcB1 / Columbia)Mutation(s): 7 
EC: 3.4.11.-
Find proteins for O96935 (Plasmodium falciparum (isolate FcB1 / Columbia))
Go to UniProtKB:  O96935
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R5V
Query on R5V

Download SDF File 
Download CCD File 
A
N-{(1R)-2-(hydroxyamino)-2-oxo-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}-2,2-dimethylpropanamide
C16 H20 N4 O3
CUWFEJVIZZQNCM-CYBMUJFWSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
R5VKi: 700 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.222α = 90.00
b = 109.593β = 90.00
c = 118.698γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
GDAdata collection
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2014-11-26
    Type: Database references