9MJW | pdb_00009mjw

Crystal structure of WRN helicase with bound allosteric fragment 3.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.263 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9MJW

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

WRN structural flexibility showcased through fragment-based lead discovery of inhibitors.

Palte, R.L.Mandal, M.Sikorska, J.Villafania, A.B.Rickard, M.M.Bauer, R.J.Buevich, A.V.Chai, X.He, J.Hussain, Z.Koglin, M.MacDonald, H.B.Mansueto, M.S.Maskos, K.Methot, J.L.Robustelli, J.Soriano, A.Tauchert, M.J.Tyagarajan, S.Zhang, M.Klein, D.J.Hicks, J.D.McLaren, D.G.Gabelli, S.B.Wyss, D.F.

(2026) Nat Commun 17: 79-79

  • DOI: https://doi.org/10.1038/s41467-025-66768-8
  • Primary Citation Related Structures: 
    9MJS, 9MJT, 9MJU, 9MJV, 9MJW, 9MJX, 9MJY, 9MJZ, 9MK0, 9MK1

  • PubMed Abstract: 

    WRN helicase is an established synthetic lethal target for inhibition in the treatment of microsatellite instability-high (MSI-H) and mismatch repair deficient (MMRd) cancers. The identification of helicase inhibitors is challenging as high-throughput biochemical screening campaigns typically return few validated hits that are often inactive in cell-based assays. Herein, we highlight the power of non-covalent fragment-based lead discovery in locating new druggable allosteric sites on WRN, enabling us to bypass the challenging behavior of WRN during high-throughput screening hampering hit identification. During the fragment optimization process, structures of WRN with key prioritized fragments reveal multiple conformations of WRN with significant domain rotations up to 180°, including a WRN conformation not previously described. Rooted in a combination of biochemical, biophysical, and structural approaches, we present the detailed analyses of optimized chemical matter evolved from screening hits and the unique ability of WRN to accommodate diverse conformations as detailed by structural characterization.


  • Organizational Affiliation
    • Discovery Chemistry, Merck & Co., Inc., MRL, Boston, MA, USA.

Macromolecule Content 

  • Total Structure Weight: 50.79 kDa 
  • Atom Count: 3,447 
  • Modeled Residue Count: 410 
  • Deposited Residue Count: 443 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN443Homo sapiensMutation(s): 0 
Gene Names: WRNRECQ3RECQL2
EC: 3.1 (PDB Primary Data), 5.6.2.4 (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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BL3
(Subject of Investigation/LOI)

Query on A1BL3



Download:Ideal Coordinates CCD File
C [auth A]6-chloro-7-methyl-1lambda~6~,2,4-benzothiadiazine-1,1,3(2H,4H)-trione
C8 H7 Cl N2 O3 S
PCSYYCUZIRSAEC-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: 2.00 Å
  • R-Value Free:  0.263 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.599α = 90
b = 62.299β = 90
c = 135.107γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
REFMACrefinement

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: 2026-01-14
    Type: Initial release
  • Version 1.1: 2026-01-21
    Changes: Database references