8RPC

Crystal structure of PfCLK3 with TCMDC-135051


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Targeting Pf CLK3 with Covalent Inhibitors: A Novel Strategy for Malaria Treatment.

Brettell, S.B.Janha, O.Begen, A.Cann, G.Sharma, S.Olaniyan, N.Yelland, T.Hole, A.J.Alam, B.Mayville, E.Gillespie, R.Capper, M.Fidock, D.A.Milligan, G.Clarke, D.J.Tobin, A.B.Jamieson, A.G.

(2024) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01300
  • Primary Citation of Related Structures:  
    8RPC

  • PubMed Abstract: 

    Malaria still causes over 600,000 deaths annually, with rising resistance to frontline drugs by Plasmodium falciparum increasing this number each year. New medicines with novel mechanisms of action are, therefore, urgently needed. In this work, we solved the cocrystal structure of the essential malarial kinase Pf CLK3 with the reversible inhibitor TCMDC-135051 ( 1 ), enabling the design of covalent inhibitors targeting a unique cysteine residue (Cys368) poorly conserved in the human kinome. Chloroacetamide 4 shows nanomolar potency and covalent inhibition in both recombinant protein and P. falciparum assays. Efficacy in parasites persisted after a 6 h washout, indicating an extended duration of action. Additionally, 4 showed improved kinase selectivity and a high selectivity index against HepG2 cells, with a low propensity for resistance (log MIR > 8.1). To our knowledge, compound 4 is the first covalent inhibitor of a malarial kinase, offering promising potential as a lead for a single-dose malaria cure.


  • Organizational Affiliation

    School of Chemistry, The Advanced Research Centre, University of Glasgow, 11 Chapel Lane, Glasgow G11 6EW, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
non-specific serine/threonine protein kinase382Plasmodium falciparumMutation(s): 0 
Gene Names: C923_03333
EC: 2.7.11.1
UniProt
Find proteins for W7JM86 (Plasmodium falciparum UGT5.1)
Explore W7JM86 
Go to UniProtKB:  W7JM86
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW7JM86
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H19 (Subject of Investigation/LOI)
Query on A1H19

Download Ideal Coordinates CCD File 
B [auth A]4-[2-[5-(diethylaminomethyl)-2-methoxy-phenyl]-1~{H}-pyrrolo[2,3-b]pyridin-4-yl]-2-propan-2-yl-benzoic acid
C29 H33 N3 O3
XKLPRHHLSQBUIC-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.627α = 90
b = 128.801β = 90
c = 108.22γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
Aimlessdata scaling
autoPROCdata processing
autoPROCdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release