5LT6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SETD2
A, B
295Homo sapiensMutation(s): 0 
Gene Names: SETD2HIF1HYPBKIAA1732KMT3ASET2HSPC069
EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt), 2.1.1.359 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYW2 (Homo sapiens)
Explore Q9BYW2 
Go to UniProtKB:  Q9BYW2
PHAROS:  Q9BYW2
GTEx:  ENSG00000181555 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYW2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
76J
Query on 76J

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
[(2~{S},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-pentyl-azanium
C20 H35 N7 O5
RFJREUSTWBSNNC-OAVPVUAOSA-P
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
H [auth B]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
H [auth B],
I [auth B],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
SCN
Query on SCN

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.36α = 90
b = 72.7β = 89.77
c = 61.86γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
BUSTERphasing

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: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations