8PFL

Crystal structure of WRN helicase domain in complex with 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of WRN inhibitor HRO761 with synthetic lethality in MSI cancers.

Ferretti, S.Hamon, J.de Kanter, R.Scheufler, C.Andraos-Rey, R.Barbe, S.Bechter, E.Blank, J.Bordas, V.Dammassa, E.Decker, A.Di Nanni, N.Dourdoigne, M.Gavioli, E.Hattenberger, M.Heuser, A.Hemmerlin, C.Hinrichs, J.Kerr, G.Laborde, L.Jaco, I.Nunez, E.J.Martus, H.J.Quadt, C.Reschke, M.Romanet, V.Schaeffer, F.Schoepfer, J.Schrapp, M.Strang, R.Voshol, H.Wartmann, M.Welly, S.Zecri, F.Hofmann, F.Mobitz, H.Cortes-Cros, M.

(2024) Nature 629: 443-449

  • DOI: https://doi.org/10.1038/s41586-024-07350-y
  • Primary Citation of Related Structures:  
    8PFL, 8PFO, 8PFP

  • PubMed Abstract: 

    The Werner syndrome RecQ helicase WRN was identified as a synthetic lethal target in cancer cells with microsatellite instability (MSI) by several genetic screens 1-6 . Despite advances in treatment with immune checkpoint inhibitors 7-10 , there is an unmet need in the treatment of MSI cancers 11-14 . Here we report the structural, biochemical, cellular and pharmacological characterization of the clinical-stage WRN helicase inhibitor HRO761, which was identified through an innovative hit-finding and lead-optimization strategy. HRO761 is a potent, selective, allosteric WRN inhibitor that binds at the interface of the D1 and D2 helicase domains, locking WRN in an inactive conformation. Pharmacological inhibition by HRO761 recapitulated the phenotype observed by WRN genetic suppression, leading to DNA damage and inhibition of tumour cell growth selectively in MSI cells in a p53-independent manner. Moreover, HRO761 led to WRN degradation in MSI cells but not in microsatellite-stable cells. Oral treatment with HRO761 resulted in dose-dependent in vivo DNA damage induction and tumour growth inhibition in MSI cell- and patient-derived xenograft models. These findings represent preclinical pharmacological validation of WRN as a therapeutic target in MSI cancers. A clinical trial with HRO761 (NCT05838768) is ongoing to assess the safety, tolerability and preliminary anti-tumour activity in patients with MSI colorectal cancer and other MSI solid tumours.


  • Organizational Affiliation

    Novartis BioMedical Research, Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN431Homo sapiensMutation(s): 6 
Gene Names: WRNRECQ3RECQL2
EC: 3.1 (PDB Primary Data), 3.6.4.12 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14191 (Homo sapiens)
Explore Q14191 
Go to UniProtKB:  Q14191
PHAROS:  Q14191
GTEx:  ENSG00000165392 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14191
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YH8 (Subject of Investigation/LOI)
Query on YH8

Download Ideal Coordinates CCD File 
C [auth A]2-[2-(3,6-dihydro-2~{H}-pyran-4-yl)-5-ethyl-7-oxidanylidene-6-[4-(3-oxidanylpyridin-2-yl)carbonylpiperazin-1-yl]-[1,2,4]triazolo[1,5-a]pyrimidin-4-yl]-~{N}-[2-methyl-4-(trifluoromethyl)phenyl]ethanamide
C32 H33 F3 N8 O5
FLRLAYBOOSONEK-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.231α = 90
b = 87.484β = 90
c = 133.878γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing

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: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Database references