4K5O | pdb_00004k5o

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

• PDB DOI: https://doi.org/10.2210/pdb4K5O/pdb

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


• Deposited: 2013-04-15 Released: 2013-06-12 
• Deposition Author(s): McGowan, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.241 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

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 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.

---

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: 105.01 kDa 
• Atom Count: 8,279 
• Modeled Residue Count: 889 
• Deposited Residue Count: 895 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
M1 family aminopeptidase	A	895	Plasmodium falciparum FcB1/Columbia	Mutation(s): 7  EC: 3.4.11
UniProt
Find proteins for O96935 (Plasmodium falciparum (isolate 3D7)) Explore O96935  Go to UniProtKB:  O96935

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1OT	G [auth A]	{(R)-amino[4-(1H-pyrazol-1-yl)phenyl]methyl}phosphonic acid C10 H12 N3 O3 P KEKSMECJAGVZSC-SNVBAGLBSA-N
GOL	B [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	C [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.241 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.056	α = 90
b = 109.35	β = 90
c = 118.518	γ = 90

Software Package:

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

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