9CVD | pdb_00009cvd

SET Domain of Histone-Lysine N-Methyltransferase NSD2 in Complex with Selective Inhibitor


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

NSD2 inhibitors rewire chromatin to treat lung and pancreatic cancers.

Jeong, J.Hausmann, S.Dong, H.Szczepski, K.Flores, N.M.Garcia Gonzalez, A.Shi, L.Lu, X.Lempiainen, J.Jakab, M.Zeng, L.Chasan, T.Bareke, E.Dong, R.Carlson, E.Padilla, R.Husmann, D.Thompson, J.Shipman, G.A.Zahn, E.Barnes, C.A.Khan, L.F.Albertorio-Saez, L.M.Brill, E.Kumary, V.U.S.Marunde, M.R.Maryanski, D.N.Szany, C.C.Venters, B.J.Windham, C.L.Nowakowski, M.E.Czaban, I.Jaremko, M.Keogh, M.C.Le, K.Soth, M.J.Garcia, B.A.Jaremko, L.Majewski, J.Mazur, P.K.Gozani, O.

(2025) Nature 

  • DOI: https://doi.org/10.1038/s41586-025-09299-y
  • Primary Citation of Related Structures:  
    9CVD

  • PubMed Abstract: 

    NSD2 catalyses the epigenetic modification H3K36me2 (refs. 1,2 ) and is a candidate convergent downstream effector of oncogenic signalling in diverse malignancies 3-5 . However, it remains unclear whether the enzymatic activity of NSD2 is therapeutically targetable. Here we characterize a series of clinical-grade small-molecule catalytic NSD2 inhibitors (NSD2i) and show that the pharmacological targeting of NSD2 constitutes an epigenetic dependency with broad therapeutic efficacy in KRAS-driven preclinical cancer models. NSD2i inhibits NSD2 with single-digit nanomolar half-maximal inhibitory concentration potency and high selectivity over related methyltransferases. Structural analyses reveal that the specificity of NSD2i for NSD2 is due to competitive binding with S-adenosylmethionine and catalytic disruption through a binary-channel obstruction mechanism. Proteo-epigenomic and single-cell strategies in pancreatic and lung cancer models support a mechanism in which sustained NSD2i exposure reverses pathological H3K36me2-driven chromatin plasticity, re-establishing silencing at H3K27me3-legacy loci to curtail oncogenic gene expression programs. Accordingly, NSD2i impairs the viability of pancreatic and lung cancer cells and the growth of patient-derived xenograft tumours. Furthermore, NSD2i, which is well-tolerated in vivo, prolongs survival in advanced-stage autochthonous KRAS G12C -driven pancreatic and lung tumours in mouse models to a comparable level as KRAS inhibition with sotorasib 6 . In these models, treatment with both a NSD2 inhibitor and sotorasib synergize to confer sustained survival with extensive tumour regression and elimination. Together, our work uncovers targeting of the NSD2-H3K36me2 axis as an actionable vulnerability in difficult to treat cancers and provides support for the evaluation of NSD2 and KRAS inhibitor combination therapies in a clinical setting.


  • Organizational Affiliation
    • Department of Biology, Stanford University, Stanford, CA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase NSD2220Homo sapiensMutation(s): 0 
Gene Names: NSD2KIAA1090MMSETTRX5WHSC1
EC: 2.1.1.357
UniProt & NIH Common Fund Data Resources
Find proteins for O96028 (Homo sapiens)
Explore O96028 
Go to UniProtKB:  O96028
PHAROS:  O96028
GTEx:  ENSG00000109685 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO96028
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentSaudi Arabiabaseline funds

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Database references
  • Version 1.2: 2025-08-20
    Changes: Database references