X-ray crystal structure of PfA-M17 in complex with hydroxamic acid-based inhibitor 10s

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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Potent dual inhibitors of Plasmodium falciparum M1 and M17 aminopeptidases through optimization of S1 pocket interactions.

Drinkwater, N.Vinh, N.B.Mistry, S.N.Bamert, R.S.Ruggeri, C.Holleran, J.P.Loganathan, S.Paiardini, A.Charman, S.A.Powell, A.K.Avery, V.M.McGowan, S.Scammells, P.J.

(2016) Eur J Med Chem 110: 43-64

  • DOI: https://doi.org/10.1016/j.ejmech.2016.01.015
  • Primary Citation of Related Structures:  
    4ZW3, 4ZW5, 4ZW6, 4ZW7, 4ZW8, 4ZX3, 4ZX4, 4ZX5, 4ZX6, 4ZX8, 4ZX9, 4ZY0, 4ZY1, 4ZY2, 4ZYQ

  • PubMed Abstract: 

    Malaria remains a global health problem, and though international efforts for treatment and eradication have made some headway, the emergence of drug-resistant parasites threatens this progress. Antimalarial therapeutics acting via novel mechanisms are urgently required. Plasmodium falciparum M1 and M17 are neutral aminopeptidases which are essential for parasite growth and development. Previous work in our group has identified inhibitors capable of dual inhibition of PfA-M1 and PfA-M17, and revealed further regions within the protease S1 pockets that could be exploited in the development of ligands with improved inhibitory activity. Herein, we report the structure-based design and synthesis of novel hydroxamic acid analogues that are capable of potent inhibition of both PfA-M1 and PfA-M17. Furthermore, the developed compounds potently inhibit Pf growth in culture, including the multi-drug resistant strain Dd2. The ongoing development of dual PfA-M1/PfA-M17 inhibitors continues to be an attractive strategy for the design of novel antimalarial therapeutics.

  • Organizational Affiliation

    Biomedicine Discovery Institute and Department of Microbiology, Melbourne, VIC 3800, Australia; Department of Biochemistry and Molecular Biology Monash University (Clayton Campus), Melbourne, VIC 3800, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable M17 family aminopeptidase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
522Plasmodium falciparum FcB1/ColumbiaMutation(s): 3 
Find proteins for A0A024V0B1 (Plasmodium falciparum Vietnam Oak-Knoll)
Explore A0A024V0B1 
Go to UniProtKB:  A0A024V0B1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A024V0B1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 4U6

Download Ideal Coordinates CCD File 
EC [auth L]
FA [auth D]
HB [auth H]
M [auth A]
MA [auth E]
EC [auth L],
FA [auth D],
HB [auth H],
M [auth A],
MA [auth E],
MB [auth I],
SA [auth F],
SB [auth J],
T [auth B],
YB [auth K],
Z [auth C],
ZA [auth G]
C20 H24 N4 O4
Query on 1PE

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CC [auth K]
DA [auth C]
DB [auth G]
EA [auth C]
EB [auth G]
CC [auth K],
DA [auth C],
DB [auth G],
EA [auth C],
EB [auth G],
FB [auth G],
IC [auth L],
JA [auth D],
KA [auth D],
LB [auth H],
Q [auth A],
QA [auth E],
QB [auth I],
R [auth A],
RA [auth E],
RB [auth I],
WA [auth F],
WB [auth J],
X [auth B],
XA [auth F]
C10 H22 O6
Query on SO4

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DC [auth K]
GB [auth G]
JC [auth L]
LA [auth D]
S [auth A]
DC [auth K],
GB [auth G],
JC [auth L],
LA [auth D],
S [auth A],
XB [auth J],
Y [auth B],
YA [auth F]
O4 S
Query on ZN

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AA [auth C]
AB [auth G]
AC [auth K]
BA [auth C]
BB [auth G]
AA [auth C],
AB [auth G],
AC [auth K],
BA [auth C],
BB [auth G],
FC [auth L],
GA [auth D],
GC [auth L],
HA [auth D],
IB [auth H],
JB [auth H],
N [auth A],
NA [auth E],
NB [auth I],
O [auth A],
OA [auth E],
OB [auth I],
TA [auth F],
TB [auth J],
U [auth B],
UA [auth F],
UB [auth J],
V [auth B],
ZB [auth K]
Query on CO3

Download Ideal Coordinates CCD File 
BC [auth K]
CA [auth C]
CB [auth G]
HC [auth L]
IA [auth D]
BC [auth K],
CA [auth C],
CB [auth G],
HC [auth L],
IA [auth D],
KB [auth H],
P [auth A],
PA [auth E],
PB [auth I],
VA [auth F],
VB [auth J],
W [auth B]
C O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.436α = 90
b = 176.565β = 90
c = 230.997γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1063786

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description