8PFL

Crystal structure of WRN helicase domain in complex with 3

• PDB DOI: https://doi.org/10.2210/pdb8PFL/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2023-06-16 Released: 2024-04-24 
• Deposition Author(s): Scheufler, C., Meyer, M., Moebitz, H.
• Funding Organization(s): Not funded

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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 

Literature

A WRN inhibitor shows anti-tumor efficacy in MSI-high tumor models

Moebitz, H., Cortes-Cros, M., Scheufler, C., Hamon, J., Strang, R., Wartmann, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 49.36 kDa 
• Atom Count: 3,695 
• Modelled Residue Count: 422 
• Deposited Residue Count: 431 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN	A	431	Homo sapiens	Mutation(s): 6  Gene Names: WRN, RECQ3, RECQL2 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YH8 (Subject of Investigation/LOI)	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	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 = 40.231	α = 90
b = 87.484	β = 90
c = 133.878	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Scheufler, C., Meyer, M., Moebitz, H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release