8HO5

Falcilysin in complex with MMV665806


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Identification of an inhibitory pocket in falcilysin provides a new avenue for malaria drug development.

Wirjanata, G.Lin, J.Dziekan, J.M.El Sahili, A.Chung, Z.Tjia, S.Binte Zulkifli, N.E.Boentoro, J.Tham, R.Jia, L.S.Go, K.D.Yu, H.Partridge, A.Olsen, D.Prabhu, N.Sobota, R.M.Nordlund, P.Lescar, J.Bozdech, Z.

(2024) Cell Chem Biol 31: 743-759.e8

  • DOI: https://doi.org/10.1016/j.chembiol.2024.03.002
  • Primary Citation of Related Structures:  
    7DI7, 7DIA, 7DIJ, 8HO4, 8HO5

  • PubMed Abstract: 

    Identification of new druggable protein targets remains the key challenge in the current antimalarial development efforts. Here we used mass-spectrometry-based cellular thermal shift assay (MS-CETSA) to identify potential targets of several antimalarials and drug candidates. We found that falcilysin (FLN) is a common binding partner for several drug candidates such as MK-4815, MMV000848, and MMV665806 but also interacts with quinoline drugs such as chloroquine and mefloquine. Enzymatic assays showed that these compounds can inhibit FLN proteolytic activity. Their interaction with FLN was explored systematically by isothermal titration calorimetry and X-ray crystallography, revealing a shared hydrophobic pocket in the catalytic chamber of the enzyme. Characterization of transgenic cell lines with lowered FLN expression demonstrated statistically significant increases in susceptibility toward MK-4815, MMV000848, and several quinolines. Importantly, the hydrophobic pocket of FLN appears amenable to inhibition and the structures reported here can guide the development of novel drugs against malaria.


  • Organizational Affiliation

    School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Falcilysin1,158Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: FLNPF3D7_1360800
EC: 3.4.24
UniProt
Find proteins for Q76NL8 (Plasmodium falciparum (isolate 3D7))
Explore Q76NL8 
Go to UniProtKB:  Q76NL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ76NL8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XUN (Subject of Investigation/LOI)
Query on XUN

Download Ideal Coordinates CCD File 
B [auth A](2S)-1-(2,3-dimethyl-1H-indol-1-yl)-3-{[(1S,2S)-2-methylcyclohexyl]amino}propan-2-ol
C20 H30 N2 O
GDDCYANZONIPGV-FNHZYXHNSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.89α = 90
b = 106.29β = 90
c = 126.91γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
Cootmodel building
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release
  • Version 2.0: 2024-05-22
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2024-07-03
    Changes: Database references