7O2I

METTL3-METTL14 heterodimer bound to the SAM competitive small molecule inhibitor STM2457


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Small-molecule inhibition of METTL3 as a strategy against myeloid leukaemia.

Yankova, E.Blackaby, W.Albertella, M.Rak, J.De Braekeleer, E.Tsagkogeorga, G.Pilka, E.S.Aspris, D.Leggate, D.Hendrick, A.G.Webster, N.A.Andrews, B.Fosbeary, R.Guest, P.Irigoyen, N.Eleftheriou, M.Gozdecka, M.Dias, J.M.L.Bannister, A.J.Vick, B.Jeremias, I.Vassiliou, G.S.Rausch, O.Tzelepis, K.Kouzarides, T.

(2021) Nature 593: 597-601

  • DOI: https://doi.org/10.1038/s41586-021-03536-w
  • Primary Citation of Related Structures:  
    7O2I

  • PubMed Abstract: 

    N 6 -methyladenosine (m 6 A) is an abundant internal RNA modification 1,2 that is catalysed predominantly by the METTL3-METTL14 methyltransferase complex 3,4 . The m 6 A methyltransferase METTL3 has been linked to the initiation and maintenance of acute myeloid leukaemia (AML), but the potential of therapeutic applications targeting this enzyme remains unknown 5-7 . Here we present the identification and characterization of STM2457, a highly potent and selective first-in-class catalytic inhibitor of METTL3, and a crystal structure of STM2457 in complex with METTL3-METTL14. Treatment of tumours with STM2457 leads to reduced AML growth and an increase in differentiation and apoptosis. These cellular effects are accompanied by selective reduction of m 6 A levels on known leukaemogenic mRNAs and a decrease in their expression consistent with a translational defect. We demonstrate that pharmacological inhibition of METTL3 in vivo leads to impaired engraftment and prolonged survival in various mouse models of AML, specifically targeting key stem cell subpopulations of AML. Collectively, these results reveal the inhibition of METTL3 as a potential therapeutic strategy against AML, and provide proof of concept that the targeting of RNA-modifying enzymes represents a promising avenue for anticancer therapy.


  • Organizational Affiliation

    Milner Therapeutics Institute, University of Cambridge, Cambridge, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N6-adenosine-methyltransferase catalytic subunit228Homo sapiensMutation(s): 0 
Gene Names: METTL3MTA70
EC: 2.1.1.348
UniProt & NIH Common Fund Data Resources
Find proteins for Q86U44 (Homo sapiens)
Explore Q86U44 
Go to UniProtKB:  Q86U44
PHAROS:  Q86U44
GTEx:  ENSG00000165819 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86U44
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
N6-adenosine-methyltransferase non-catalytic subunit291Homo sapiensMutation(s): 0 
Gene Names: METTL14KIAA1627
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCE5 (Homo sapiens)
Explore Q9HCE5 
Go to UniProtKB:  Q9HCE5
PHAROS:  Q9HCE5
GTEx:  ENSG00000145388 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HCE5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V22 (Subject of Investigation/LOI)
Query on V22

Download Ideal Coordinates CCD File 
C [auth A]~{N}-[[6-[(cyclohexylmethylamino)methyl]imidazo[1,2-a]pyridin-2-yl]methyl]-4-oxidanylidene-1~{H}-pyrido[1,2-a]pyrimidine-2-carboxamide
C25 H29 N6 O2
SUWOYRGBAIBWQL-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
D [auth B]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.186 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.094α = 90
b = 64.094β = 90
c = 225.302γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references
  • Version 1.2: 2021-06-09
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Database references, Derived calculations, Refinement description