9S89 | pdb_00009s89

N-terminal 40kDa fragment of human PMS2 with covalent ligand NP1867

• PDB DOI: https://doi.org/10.2210/pdb9S89/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-08-05 Released: 2026-06-03 
• Deposition Author(s): Nichols, C.E., Carr, K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.229 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.212 (DCC) 

Starting Model: experimental

Literature

Pharmacologic Inhibition of PMS2 Induces MMR Deficiency and Response to Immune Checkpoint Blockade.

Blagg, J., Riou, P., Hervieu, A., Piumatti, E., Rodriguez-Plata, M.T., Battuello, P., Peall, A., Amodio, V., Vitiello, P.P., Nightingale, D.J.H., Bago, R., Tongue, P., Slater, T., Parmar, K., Patel, P., Rodriguez Gonzalez, J., Clark, D.E., Langley, G.W., Nichols, C., Guarne, A., Winship, P.C.M., Baker, M., Drysdale, M., Germano, G., Bardelli, A.

(2026) Cancer Discov 16: 1649-1665

• PubMed: 42013405 
• DOI: https://doi.org/10.1158/2159-8290.CD-26-0003
• Primary Citation Related Structures: 
  9PRP, 9S89


• PubMed Abstract: 
  

  DNA mismatch repair (MMR) detects and corrects postreplicative DNA alterations; it is deregulated in up to 20% of human cancers. MMR-deficient (MMR-d) cancers display increased tumor mutational burden (TMB) and microsatellite instability (MSI) and are eligible for checkpoint inhibitor (CPI) immunotherapy which commonly elicits durable responses. We reasoned that pharmacologic blockade of MMR could broaden the patient population eligible for immunotherapy. Here, we reveal MMR protein PMS2 as a druggable target and describe the discovery and characterization of first-in-class small-molecule MMR pathway modulator NP1867. In vitro treatment of murine cancer cells abrogates MMR function and elicits an MMR-d genotype, including increased TMB, MMR-d mutational signatures, and MSI-high (MSI-H) status. Inoculation of syngeneic immunocompetent mice with cancer cells pretreated with NP1867 leads to CPI sensitivity, tumor growth delay, and complete responses. For the first time, we demonstrate pharmacologic targeting of MMR to proactively rewire the tumor-host relationship for therapeutic purposes. We present the discovery and characterization of NP1867, a selective covalent small-molecule inhibitor of MMR protein PMS2. Pharmacologic blockade of PMS2 leads to an MMR-deficient genotype characterized by increased TMB, enriched MMR-d mutational signatures, and MSI-H status. Treatment with NP1867 converts immunoresistant, MMR-proficient cancers into CPI-responsive tumors. See related commentary by Bernards, p. 1486.

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Organizational Affiliation: 
• NeoPhore Ltd, Altrincham, United Kingdom.
IFOM ETS - The AIRC Institute of Molecular Oncology , Milan, Italy.
Department of Oncology, Molecular Biotechnology Center, University of Torino, Turin, Italy.
Charnwood Discovery, Loughborough, United Kingdom.
Charles River Laboratories, Saffron Walden, United Kingdom.
o2h Discovery Pvt Ltd, Ahmedabad, India.
Department of Biochemistry, Centre de Recherche en Biologie Structurale, McGill University, Montreal, Canada.
Department of Medical Biotechnology and Translational Medicine, University of Milano, Milan, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.43 kDa 
• Atom Count: 2,404 
• Modeled Residue Count: 288 
• Deposited Residue Count: 367 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mismatch repair endonuclease PMS2	A	367	Homo sapiens	Mutation(s): 0  Gene Names: PMS2, PMSL2 EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P54278 (Homo sapiens) Explore P54278  Go to UniProtKB:  P54278
PHAROS:  P54278 GTEx:  ENSG00000122512

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JMJ (Subject of Investigation/LOI)	F [auth A]	~{N}-[2-[2-(cyclohexylmethoxy)-3-methyl-4,6-bis(oxidanyl)phenyl]carbonyl-1,3-dihydroisoindol-4-yl]-4-(dimethylamino)butanamide C29 H39 N3 O5 TWCKDBBYCLWELT-UHFFFAOYSA-N
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.229 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.212 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.292	α = 90
b = 82.292	β = 90
c = 110.801	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-03 
Deposition Author(s): Nichols, C.E., Carr, K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-06-03
  Type: Initial release
  
• Version 1.1: 2026-08-12
  Changes: Database references