4K5M

Phosphonic Arginine Mimetics as Inhibitors of the M1 Aminopeptidases from Plasmodium falciparum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Synthesis and Structure-Activity Relationships of Phosphonic Arginine Mimetics as Inhibitors of the M1 and M17 Aminopeptidases from Plasmodium falciparum.

Kannan Sivaraman, K.Paiardini, A.Sienczyk, M.Ruggeri, C.Oellig, C.A.Dalton, J.P.Scammells, P.J.Drag, M.McGowan, S.

(2013) J.Med.Chem. 56: 5213-5217

  • DOI: 10.1021/jm4005972
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The malaria parasite Plasmodium falciparum employs two metallo-aminopeptidases, PfA-M1 and PfA-M17, which are essential for parasite survival. Compounds that inhibit the activity of either enzyme represent leads for the development of new antimalaria ...

    The malaria parasite Plasmodium falciparum employs two metallo-aminopeptidases, PfA-M1 and PfA-M17, which are essential for parasite survival. Compounds that inhibit the activity of either enzyme represent leads for the development of new antimalarial drugs. Here we report the synthesis and structure-activity relationships of a small library of phosphonic acid arginine mimetics that probe the S1 pocket of both enzymes and map the necessary interactions that would be important for a dual inhibitor.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, VIC 3800, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
M1 family aminopeptidase
A
898Plasmodium 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
1OV
Query on 1OV

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Download CCD File 
A
[(1R)-1-amino-4-carbamimidamidobutyl]phosphonic acid
C5 H15 N4 O3 P
MMEPWCMDQUSOLC-SCSAIBSYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1OVKi: 193000 nM BINDINGMOAD
1OVKi: 193000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.995α = 90.00
b = 109.035β = 90.00
c = 118.576γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
Blu-Icedata collection
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-04-14 
  • Released Date: 2013-06-12 
  • Deposition Author(s): McGowan, S.

Revision History 

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2013-07-24
    Type: Database references