4K5L

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

• PDB DOI: https://doi.org/10.2210/pdb4K5L/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Plasmodium falciparum FcB1/Columbia
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.220 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Starting Model: experimental

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

• PubMed: 23713488 
• DOI: https://doi.org/10.1021/jm4005972
• Primary Citation of Related Structures:  
  4K3N, 4K5L, 4K5M, 4K5N, 4K5O, 4K5P


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 105.15 kDa 
• Atom Count: 7,872 
• Modelled Residue Count: 889 
• Deposited Residue Count: 898 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
M1 family aminopeptidase	A	898	Plasmodium falciparum FcB1/Columbia	Mutation(s): 7  EC: 3.4.11
UniProt
Find proteins for O96935 (Plasmodium falciparum (isolate 3D7)) Go to UniProtKB:  O96935

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
19N	C [auth A]	[(1R)-1-amino-5-carbamimidamidopentyl]phosphonic acid C6 H17 N4 O3 P GAZYHWYZAQCLLA-RXMQYKEDSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
19N	PDBBind:  4K5L	Ki: 1.10e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.220 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.094	α = 90
b = 109.345	β = 90
c = 118.706	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description