9RUS | pdb_00009rus

Structure of WRN in complex with ATPgS and Compound 3

PDB DOI: https://doi.org/10.2210/pdb9RUS/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-07-04 Released: 2025-10-22
Deposition Author(s): Fletcher, C.T., Rucktooa, P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.298 (Depositor), 0.280 (DCC)
R-Value Work:
0.267 (Depositor)
R-Value Observed:
0.269 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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.

(2026) Bioorg Med Chem Lett 131: 130421-130421

PubMed: 41038585 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2025.130421
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 99.9 kDa
Atom Count: 7,456
Modeled Residue Count: 806
Deposited Residue Count: 854
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN	A, B	427	Homo sapiens	Mutation(s): 0 Gene Names: WRN, RECQ3, RECQL2 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14191
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS Query on AGS Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain C [auth A]	C [auth A], L [auth B]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain H [auth A]	H [auth A], N [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth B]
GQP (Subject of Investigation/LOI) Query on GQP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	1-[(4-fluorophenyl)methyl]benzimidazole C₁₄ H₁₁ F N₂ QLQZBMMYHJKDSH-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], O [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain J [auth A]	J [auth A], P [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain P [auth B] Interactions & Density Focus chain J [auth A] Focus chain P [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	G [auth A], I [auth A], M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain M [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]