6EE2 | pdb_00006ee2

X-ray crystal structure of Pf-M17 in complex with inhibitor 6i and regulatory zinc ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.240 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6EE2

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases.

Vinh, N.B.Drinkwater, N.Malcolm, T.R.Kassiou, M.Lucantoni, L.Grin, P.M.Butler, G.S.Duffy, S.Overall, C.M.Avery, V.M.Scammells, P.J.McGowan, S.

(2019) J Med Chem 62: 622-640

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01310
  • Primary Citation Related Structures: 
    6EA1, 6EA2, 6EAA, 6EAB, 6EE2, 6EE3, 6EE4, 6EE6, 6EED, 6EEE

  • PubMed Abstract: 

    There is an urgent clinical need for antimalarial compounds that target malaria caused by both Plasmodium falciparum and Plasmodium vivax. The M1 and M17 metalloexopeptidases play key roles in Plasmodium hemoglobin digestion and are validated drug targets. We used a multitarget strategy to rationally design inhibitors capable of potent inhibition of the M1 and M17 aminopeptidases from both P. falciparum ( Pf-M1 and Pf-M17) and P. vivax ( Pv-M1 and Pv-M17). The novel chemical series contains a hydroxamic acid zinc binding group to coordinate catalytic zinc ion/s, and a variety of hydrophobic groups to probe the S1' pockets of the four target enzymes. Structural characterization by cocrystallization showed that selected compounds utilize new and unexpected binding modes; most notably, compounds substituted with bulky hydrophobic substituents displace the Pf-M17 catalytic zinc ion. Excitingly, key compounds of the series potently inhibit all four molecular targets and show antimalarial activity comparable to current clinical candidates.


  • Organizational Affiliation
    • Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences , Monash University, Parkville , Melbourne , VIC 3052 , Australia.

Macromolecule Content 

  • Total Structure Weight: 719.51 kDa 
  • Atom Count: 52,312 
  • Modeled Residue Count: 6,189 
  • Deposited Residue Count: 6,312 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pf-M17
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
526Plasmodium falciparum NF135/5.C10Mutation(s): 3 
Gene Names: PFNF135_05834
EC: 3.4.11.1
UniProt
Find proteins for W4I9J7 (Plasmodium falciparum NF135/5.C10)
Explore W4I9J7 
Go to UniProtKB:  W4I9J7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW4I9J7
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J1V
(Subject of Investigation/LOI)

Query on J1V



Download:Ideal Coordinates CCD File
AA [auth B]
EC [auth I]
HA [auth C]
HB [auth F]
HD [auth L]
AA [auth B],
EC [auth I],
HA [auth C],
HB [auth F],
HD [auth L],
O [auth A],
OA [auth D],
OB [auth G],
OC [auth J],
VC [auth K],
YA [auth E],
ZB [auth H]
N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]cyclohexanecarboxamide
C21 H21 F3 N2 O3
FVWBWBSCYLNPGK-LJQANCHMSA-N
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
AB [auth E]
AC [auth H]
AD [auth K]
BA [auth B]
BB [auth E]
AB [auth E],
AC [auth H],
AD [auth K],
BA [auth B],
BB [auth E],
BC [auth H],
CA [auth B],
ED [auth L],
FC [auth I],
GC [auth I],
HC [auth I],
IA [auth C],
JA [auth C],
JB [auth F],
JD [auth L],
KB [auth F],
KD [auth L],
LB [auth F],
LD [auth L],
MD [auth L],
PC [auth J],
QC [auth J],
R [auth A],
RA [auth D],
RB [auth G],
RC [auth J],
S [auth A],
SA [auth D],
SB [auth G],
TA [auth D],
TB [auth G],
UA [auth D],
UB [auth G],
XC [auth K],
YC [auth K],
ZA [auth E],
ZC [auth K]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
CD [auth K]
DB [auth E]
DD [auth K]
EA [auth B]
EB [auth E]
CD [auth K],
DB [auth E],
DD [auth K],
EA [auth B],
EB [auth E],
IB [auth F],
ID [auth L],
KC [auth I],
LA [auth C],
LC [auth I],
ND [auth L],
OD [auth L],
P [auth A],
PA [auth D],
PB [auth G],
Q [auth A],
QA [auth D],
QB [auth G],
T [auth A],
W [auth A],
WB [auth G],
WC [auth K],
X [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS

Query on DMS



Download:Ideal Coordinates CCD File
BD [auth K]
CB [auth E]
DA [auth B]
KA [auth C]
SC [auth J]
BD [auth K],
CB [auth E],
DA [auth B],
KA [auth C],
SC [auth J],
U [auth A],
V [auth A],
VA [auth D],
VB [auth G]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
CC [auth I]
GA [auth C]
GB [auth F]
GD [auth L]
N [auth A]
CC [auth I],
GA [auth C],
GB [auth F],
GD [auth L],
N [auth A],
NA [auth D],
NB [auth G],
NC [auth J],
UC [auth K],
XA [auth E],
YB [auth H],
Z [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
IC [auth I],
JC [auth I]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CO3

Query on CO3



Download:Ideal Coordinates CCD File
DC [auth I]
FA [auth C]
FB [auth F]
FD [auth L]
M [auth A]
DC [auth I],
FA [auth C],
FB [auth F],
FD [auth L],
M [auth A],
MA [auth D],
MB [auth G],
MC [auth J],
TC [auth K],
WA [auth E],
XB [auth H],
Y [auth B]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.240 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.183α = 90
b = 177.867β = 90
c = 229.645γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

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
Australian Research Council (ARC)AustraliaFT100100690

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations