9RUR | pdb_00009rur

Structure of WRN in complex with ATPgS and covalent ligand Compound 4d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.281 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 
    0.252 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

AI-assisted delivery of novel covalent WRN inhibitors from a non-covalent fragment screen.

Smith, G.M.T.Aithani, L.Barrett, C.E.Bucher, A.O.Cooper, C.D.O.Degorce, S.L.Dore, A.S.Fletcher, C.T.Huber, S.Huckvale, R.Kennedy, A.J.Mornement, A.A.Pickworth, M.Rucktooa, P.Scully, C.C.G.Skerratt, S.E.

(2025) Bioorg Med Chem Lett : 130421-130421

  • DOI: https://doi.org/10.1016/j.bmcl.2025.130421
  • Primary Citation of Related Structures:  
    9RTI, 9RUR, 9RUS

  • PubMed Abstract: 

    Werner (WRN) helicase, has emerged as a promising therapeutic target for cancers associated with microsatellite instability (MSI). This letter describes the discovery of small molecule inhibitors from a fragment screen that occupy a cryptic, allosteric site of WRN helicase. Key findings include the identification of benzimidazole and amino-indazole scaffolds, exploiting their proximity to Cys727 via covalent modification. The use of our proprietary co-folding model DragonFold assisted the identification of novel WRN helicase inhibitors. These, together with near-neighbor profiling, offer tools for furthering the understanding of WRN and BLM helicase function, and potential therapeutic avenues for MSI-associated cancers.


  • Organizational Affiliation
    • CHARM Therapeutics Ltd., B900, Babraham Research Campus, Babraham, Cambridge, CB22 3AT, UK.. Electronic address: geoffrey@charmtx.com.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
A, B
427Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download Ideal Coordinates CCD File 
C [auth A],
N [auth B]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
I [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
A1JJK (Subject of Investigation/LOI)
Query on A1JJK

Download Ideal Coordinates CCD File 
H [auth A]2-ethylsulfanyl-~{N}-[1-[(4-fluorophenyl)methyl]indazol-3-yl]ethanamide
C18 H18 F N3 O S
NOBRUCRPWOWGNN-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
J [auth A],
P [auth B],
Q [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
M [auth A],
U [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
K [auth A]
L [auth A]
O [auth B]
F [auth A],
G [auth A],
K [auth A],
L [auth A],
O [auth B],
R [auth B],
S [auth B],
T [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
V [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.281 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 0.252 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.98α = 90
b = 89.98β = 90
c = 241.352γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2025-10-22
    Type: Initial release