9RTI | pdb_00009rti

Structure of WRN in complex with ATPgS and covalent ligand Compound 7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.274 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 
    0.247 (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 WRN427Homo 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 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
A1JJ8 (Subject of Investigation/LOI)
Query on A1JJ8

Download Ideal Coordinates CCD File 
K [auth A]~{N}-[1-[(4-fluorophenyl)methyl]-7-methyl-indazol-3-yl]propanamide
C18 H18 F N3 O
AFOUNTVOEGAGCF-UHFFFAOYSA-N
A1JJQ (Subject of Investigation/LOI)
Query on A1JJQ

Download Ideal Coordinates CCD File 
O [auth A]~{N}-[1-[(4-fluorophenyl)methyl]-7-methyl-indazol-3-yl]prop-2-enamide
C18 H16 F N3 O
GYEFUDDVJWTYEA-UHFFFAOYSA-N
MLT
Query on MLT

Download Ideal Coordinates CCD File 
P [auth A]D-MALATE
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth A],
Q [auth A],
U [auth A],
V [auth A],
Y [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A],
Z [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth A],
M [auth A],
N [auth A],
R [auth A],
S [auth A],
T [auth A],
W [auth A],
X [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.274 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.018α = 90
b = 122.018β = 90
c = 104.88γ = 120
Software Package:
Software NamePurpose
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
BUSTERrefinement
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