4ZY2 | pdb_00004zy2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.239 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4ZY2

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 714.86 kDa 
  • Atom Count: 52,900 
  • Modeled Residue Count: 6,185 
  • Deposited Residue Count: 6,264 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 
EC: 3.4.11.1
UniProt
Find proteins for A0A0L7M119 (Plasmodium falciparum (isolate Dd2))
Explore A0A0L7M119 
Go to UniProtKB:  A0A0L7M119
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0L7M119
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4TL

Query on 4TL



Download:Ideal Coordinates CCD File
DB [auth E]
HC [auth H]
HD [auth J]
LA [auth C]
NB [auth F]
DB [auth E],
HC [auth H],
HD [auth J],
LA [auth C],
NB [auth F],
PD [auth K],
T [auth A],
UA [auth D],
WC [auth I],
XD [auth L],
Y [auth B],
ZB [auth G]
N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluorobiphenyl-4-yl)ethyl]-2,2-dimethylpropanamide
C19 H19 F3 N2 O3
WUJRZUJJQZMYBN-MRXNPFEDSA-N
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
AA [auth B]
AC [auth G]
BB [auth E]
BC [auth G]
CB [auth E]
AA [auth B],
AC [auth G],
BB [auth E],
BC [auth G],
CB [auth E],
DD [auth J],
EB [auth E],
ED [auth J],
FD [auth J],
GD [auth J],
JA [auth C],
JC [auth H],
KA [auth C],
KB [auth F],
KC [auth H],
LB [auth F],
MB [auth F],
MD [auth K],
ND [auth K],
OB [auth F],
OD [auth K],
PB [auth F],
QA [auth D],
R [auth A],
RA [auth D],
S [auth A],
SA [auth D],
TA [auth D],
TC [auth I],
UC [auth I],
UD [auth L],
VC [auth I],
VD [auth L],
WB [auth G],
WD [auth L],
XB [auth G],
YB [auth G],
Z [auth B],
ZD [auth L]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AB [auth E]
AD [auth J]
BD [auth J]
CD [auth J]
EA [auth C]
AB [auth E],
AD [auth J],
BD [auth J],
CD [auth J],
EA [auth C],
FA [auth C],
FC [auth H],
GA [auth C],
GC [auth H],
HA [auth C],
IA [auth C],
IB [auth F],
JB [auth F],
LD [auth K],
OC [auth I],
P [auth A],
PA [auth D],
PC [auth I],
Q [auth A],
QC [auth I],
RC [auth I],
SC [auth I],
TB [auth G],
TD [auth L],
UB [auth G],
VB [auth G],
YA [auth E],
ZA [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS

Query on DMS



Download:Ideal Coordinates CCD File
IC [auth H],
U [auth A],
YD [auth L]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
BA [auth C]
CC [auth H]
DA [auth C]
EC [auth H]
FB [auth F]
BA [auth C],
CC [auth H],
DA [auth C],
EC [auth H],
FB [auth F],
HB [auth F],
ID [auth K],
KD [auth K],
LC [auth I],
M [auth A],
MA [auth D],
NC [auth I],
O [auth A],
OA [auth D],
QB [auth G],
QD [auth L],
SB [auth G],
SD [auth L],
V [auth B],
VA [auth E],
X [auth B],
XA [auth E],
XC [auth J],
ZC [auth J]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO3

Query on CO3



Download:Ideal Coordinates CCD File
CA [auth C]
DC [auth H]
GB [auth F]
JD [auth K]
MC [auth I]
CA [auth C],
DC [auth H],
GB [auth F],
JD [auth K],
MC [auth I],
N [auth A],
NA [auth D],
RB [auth G],
RD [auth L],
W [auth B],
WA [auth E],
YC [auth J]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.239 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.06α = 90
b = 177.247β = 90
c = 230.773γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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