NSD2-PWWP1 domain bound with an imidazol-5-yl benzonitrile compound

Experimental Data Snapshot

  • Resolution: 3.09 Å
  • R-Value Free: 0.345 
  • R-Value Work: 0.292 
  • R-Value Observed: 0.294 

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This is version 1.3 of the entry. See complete history


Structure-Based Discovery of a Series of NSD2-PWWP1 Inhibitors.

Li, N.Yang, H.Liu, K.Zhou, L.Huang, Y.Cao, D.Li, Y.Sun, Y.Yu, A.Du, Z.Yu, F.Zhang, Y.Wang, B.Geng, M.Li, J.Xiong, B.Xu, S.Huang, X.Liu, T.

(2022) J Med Chem 65: 9459-9477

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00709
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Overexpression, point mutations, or translocations of protein lysine methyltransferase NSD2 occur in many types of cancer cells. Therefore, it was recognized as onco-protein and considered as a promising anticancer drug target. NSD2 consists of multiple domains including a SET catalytic domain and two PWWP domains binding to methylated histone proteins. Here, we reported our efforts to develop a series of NSD2-PWWP1 inhibitors, and further structure-based optimization resulted in a potent inhibitor 38 , which has high selectivity toward the NSD2-PWWP1 domain. The detailed biological evaluation revealed that compound 38 can bind to NSD2-PWWP1 and then affect the expression of genes regulated by NSD2. The current discovery will provide a useful chemical probe to the future research in understanding the specific regulation mode of NSD2 by PWWP1 recognition and pave the way to develop potential drugs targeting NSD2 protein.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase NSD2
A, B, C
132Homo sapiensMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7QC (Subject of Investigation/LOI)
Query on 7QC

Download Ideal Coordinates CCD File 
D [auth B]4-[5-[4-(aminomethyl)-2,6-dimethoxy-phenyl]-3-methyl-imidazol-4-yl]benzenecarbonitrile
C20 H20 N4 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 3.09 Å
  • R-Value Free: 0.345 
  • R-Value Work: 0.292 
  • R-Value Observed: 0.294 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.12α = 90
b = 70.12β = 90
c = 230.67γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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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: 2022-07-06
    Type: Initial release
  • Version 1.1: 2022-07-13
    Changes: Database references
  • Version 1.2: 2022-07-27
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description