6EEE | pdb_00006eee

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.246 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6EEE

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: 707.99 kDa 
  • Atom Count: 50,000 
  • Modeled Residue Count: 6,162 
  • Deposited Residue Count: 6,228 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
M17 LEUCYL-AMINOPEPTIDASE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
519Plasmodium falciparum HB3Mutation(s): 3 
Gene Names: PFHG_04072
EC: 3.4.11.1
UniProt
Find proteins for A0A0L7KHE6 (Plasmodium falciparum (isolate HB3))
Explore A0A0L7KHE6 
Go to UniProtKB:  A0A0L7KHE6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0L7KHE6
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J4V

Query on J4V



Download:Ideal Coordinates CCD File
AB [auth F]
CC [auth I]
EA [auth C]
JB [auth G]
JD [auth L]
AB [auth F],
CC [auth I],
EA [auth C],
JB [auth G],
JD [auth L],
LC [auth J],
M [auth A],
MA [auth D],
SB [auth H],
UA [auth E],
W [auth B],
WC [auth K]
(1R,2r,3S,5R,7R)-N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]tricyclo[3.3.1.1~3,7~]decane-2-carboxamide
C25 H25 F3 N2 O3
CETVPXTYHVOGCT-YMWQUUDPSA-N
2PE

Query on 2PE



Download:Ideal Coordinates CCD File
YB [auth H]NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
DA [auth B]
HB [auth F]
HD [auth K]
IB [auth F]
ID [auth K]
DA [auth B],
HB [auth F],
HD [auth K],
IB [auth F],
ID [auth K],
JC [auth I],
KA [auth C],
KC [auth I],
LA [auth C],
PD [auth L],
QB [auth G],
QD [auth L],
RB [auth G],
RD [auth L],
SA [auth D],
SD [auth L],
TA [auth D],
TC [auth J],
U [auth A],
UC [auth J],
V [auth A],
VC [auth J],
ZB [auth H]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AD [auth K]
BD [auth K]
CD [auth K]
DB [auth F]
EB [auth F]
AD [auth K],
BD [auth K],
CD [auth K],
DB [auth F],
EB [auth F],
FC [auth I],
GC [auth I],
HA [auth C],
HC [auth I],
IA [auth C],
JA [auth C],
MB [auth G],
MD [auth L],
NB [auth G],
ND [auth L],
OC [auth J],
P [auth A],
PA [auth D],
PC [auth J],
Q [auth A],
QA [auth D],
R [auth A],
RA [auth D],
S [auth A],
VB [auth H],
WB [auth H],
XA [auth E],
XB [auth H],
YA [auth E],
Z [auth B],
ZC [auth K]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS

Query on DMS



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
BC [auth H]
CA [auth B]
OB [auth G]
AA [auth B],
BA [auth B],
BC [auth H],
CA [auth B],
OB [auth G],
T [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
CB [auth F]
EC [auth I]
GA [auth C]
LB [auth G]
LD [auth L]
CB [auth F],
EC [auth I],
GA [auth C],
LB [auth G],
LD [auth L],
NC [auth J],
O [auth A],
OA [auth D],
UB [auth H],
WA [auth E],
Y [auth B],
YC [auth K]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AC [auth H]
DD [auth K]
ED [auth K]
FB [auth F]
FD [auth K]
AC [auth H],
DD [auth K],
ED [auth K],
FB [auth F],
FD [auth K],
GB [auth F],
GD [auth K],
IC [auth I],
OD [auth L],
PB [auth G],
QC [auth J],
RC [auth J],
SC [auth J],
ZA [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CO3

Query on CO3



Download:Ideal Coordinates CCD File
BB [auth F]
DC [auth I]
FA [auth C]
KB [auth G]
KD [auth L]
BB [auth F],
DC [auth I],
FA [auth C],
KB [auth G],
KD [auth L],
MC [auth J],
N [auth A],
NA [auth D],
TB [auth H],
VA [auth E],
X [auth B],
XC [auth K]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.246 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.68α = 90
b = 177.395β = 90
c = 229.445γ = 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