9FOC | pdb_00009foc

Crystal structure of the PWWP1 domain of NSD2 bound by compound 11.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 
    0.255 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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Literature

Structural and Molecular Insight into the PWWP1 Domain of NSD2 from the Discovery of Novel Binders Via DNA-Encoded Library Screening.

Collie, G.W., Ackroyd, B., Corbishley, C., O'Donovan, D.H., Edwards, A., Gohlke, A., Guo, X., Howells, B., Li, Y., Madin, A., Milbradt, A.G., Rivers, E.L., Talapatra, S.K., Underwood, E., Webb, A.

(2025) ACS Med Chem Lett 16: 1703-1708

  • DOI: https://doi.org/10.1021/acsmedchemlett.5c00396
  • Primary Citation of Related Structures:  
    9FOC, 9FOE

  • PubMed Abstract: 

    NSD2 is a key epigenetic regulator and has received considerable attention as a drug target due to its well-documented role in tumorigenesis. We report here a DNA-encoded library screen targeting the PWWP1 domain of NSD2 from which we discovered novel, potent, and selective binders. Furthermore, these compounds were used to develop a novel crystal system, increasing our understanding of the folding of this domain. Together, these results provide a solid molecular and structural basis for the further study of the PWWP1 domain of NSD2 as a cancer drug target.

    • Organizational Affiliation: 
    • Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase NSD2
A, B
176Homo sapiensMutation(s): 0 
Gene Names: NSD2, KIAA1090, MMSET, TRX5, WHSC1
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
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IEG
Query on A1IEG
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]		(2S)-1-[4-[[(3S)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-N-methyl-pyrrolidine-2-carboxamide
C17 H27 N5 O3 S
FPDVOQXTUVFQHW-KBPBESRZSA-N
A1IFS (Subject of Investigation/LOI)
Query on A1IFS
Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]		(2S)-1-[4-[[(3R)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-N-methyl-pyrrolidine-2-carboxamide
C17 H27 N5 O3 S
FPDVOQXTUVFQHW-KGLIPLIRSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free:  0.255 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.63α = 90
b = 67.96β = 90
c = 159.69γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2025-09-03 
    • Deposition Author(s): Collie, G.W.
Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-10-01
    Changes: Database references