Structure of the m17 leucyl aminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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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: https://doi.org/10.1021/jm501323a
  • Primary Citation of Related Structures:  
    4R5T, 4R5V, 4R5X, 4R6T, 4R76, 4R7M

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
M17 family aminopeptidase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
528Plasmodium falciparum FcB1/ColumbiaMutation(s): 0 
Find proteins for Q8IL11 (Plasmodium falciparum (isolate 3D7))
Explore Q8IL11 
Go to UniProtKB:  Q8IL11
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IL11
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on R5X

Download Ideal Coordinates CCD File 
BA [auth C]
CC [auth L]
FA [auth D]
FB [auth H]
JA [auth E]
BA [auth C],
CC [auth L],
FA [auth D],
FB [auth H],
JA [auth E],
LB [auth I],
P [auth A],
RA [auth F],
RB [auth J],
V [auth B],
WB [auth K],
ZA [auth G]
C18 H17 N5 O3
Query on 1PE

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AB [auth G]
BB [auth G]
DC [auth L]
HB [auth H]
LA [auth E]
AB [auth G],
BB [auth G],
DC [auth L],
HB [auth H],
LA [auth E],
MA [auth E],
MB [auth I],
NB [auth I],
SA [auth F],
SB [auth J],
TA [auth F],
UA [auth F],
W [auth B],
X [auth B],
YB [auth K]
C10 H22 O6
Query on SO4

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GB [auth H]
KA [auth E]
NA [auth E]
Q [auth A]
R [auth A]
GB [auth H],
KA [auth E],
NA [auth E],
Q [auth A],
R [auth A],
VA [auth F],
XB [auth K]
O4 S
Query on ZN

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AA [auth C]
BC [auth L]
CA [auth D]
CB [auth H]
EA [auth D]
AA [auth C],
BC [auth L],
CA [auth D],
CB [auth H],
EA [auth D],
EB [auth H],
GA [auth E],
IA [auth E],
IB [auth I],
KB [auth I],
M [auth A],
O [auth A],
OA [auth F],
OB [auth J],
QA [auth F],
QB [auth J],
S [auth B],
TB [auth K],
U [auth B],
VB [auth K],
WA [auth G],
Y [auth C],
YA [auth G],
ZB [auth L]
Query on CO3

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AC [auth L]
DA [auth D]
DB [auth H]
HA [auth E]
JB [auth I]
AC [auth L],
DA [auth D],
DB [auth H],
HA [auth E],
JB [auth I],
N [auth A],
PA [auth F],
PB [auth J],
T [auth B],
UB [auth K],
XA [auth G],
Z [auth C]
C O3
Binding Affinity Annotations 
IDSourceBinding Affinity
R5X Binding MOAD:  4R76 Ki: 14 (nM) from 1 assay(s)
BindingDB:  4R76 Ki: 0.01 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.041α = 90
b = 177.408β = 90
c = 231.77γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
GDAdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2014-11-26
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description