Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives

Experimental Data Snapshot

  • Resolution: 2.14 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 

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Structure of the Epigenetic Oncogene MMSET and Inhibition by N-Alkyl Sinefungin Derivatives.

Tisi, D.Chiarparin, E.Tamanini, E.Pathuri, P.Coyle, J.E.Hold, A.Holding, F.P.Amin, N.Martin, A.C.Rich, S.J.Berdini, V.Yon, J.Acklam, P.Burke, R.Drouin, L.Harmer, J.E.Jeganathan, F.van Montfort, R.L.Newbatt, Y.Tortorici, M.Westlake, M.Wood, A.Hoelder, S.Heightman, T.D.

(2016) ACS Chem Biol 11: 3093-3105

  • DOI: https://doi.org/10.1021/acschembio.6b00308
  • Primary Citation of Related Structures:  
    5LSS, 5LSU, 5LSX, 5LSY, 5LSZ, 5LT6, 5LT7, 5LT8

  • PubMed Abstract: 

    The members of the NSD subfamily of lysine methyl transferases are compelling oncology targets due to the recent characterization of gain-of-function mutations and translocations in several hematological cancers. To date, these proteins have proven intractable to small molecule inhibition. Here, we present initial efforts to identify inhibitors of MMSET (aka NSD2 or WHSC1) using solution phase and crystal structural methods. On the basis of 2D NMR experiments comparing NSD1 and MMSET structural mobility, we designed an MMSET construct with five point mutations in the N-terminal helix of its SET domain for crystallization experiments and elucidated the structure of the mutant MMSET SET domain at 2.1 Å resolution. Both NSD1 and MMSET crystal systems proved resistant to soaking or cocrystallography with inhibitors. However, use of the close homologue SETD2 as a structural surrogate supported the design and characterization of N-alkyl sinefungin derivatives, which showed low micromolar inhibition against both SETD2 and MMSET.

  • Organizational Affiliation

    Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road, Cambridge, United Kingdom CB4 0QA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase NSD2
A, B
252Homo sapiensMutation(s): 5 
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
Experimental Data & Validation

Experimental Data

  • Resolution: 2.14 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.583α = 90
b = 63.114β = 90
c = 81.094γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description