6TU1

Crystal structure of the human METTL3-METTL14 complex bound to Compound 8 (ASI_M3M_091)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Small-Molecule Inhibitors of METTL3, the Major Human Epitranscriptomic Writer.

Bedi, R.K.Huang, D.Eberle, S.A.Wiedmer, L.Sledz, P.Caflisch, A.

(2020) ChemMedChem 15: 744-748

  • DOI: https://doi.org/10.1002/cmdc.202000011
  • Primary Citation of Related Structures:  
    6TTP, 6TTT, 6TTV, 6TTW, 6TTX, 6TU1, 6Y4G

  • PubMed Abstract: 

    The RNA methylase METTL3 catalyzes the transfer of a methyl group from the cofactor S-adenosyl-L-methionine (SAM) to the N 6 atom of adenine. We have screened a library of 4000 analogues and derivatives of the adenosine moiety of SAM by high-throughput docking into METTL3. Two series of adenine derivatives were identified in silico, and the binding mode of six of the predicted inhibitors was validated by protein crystallography. Two compounds, one for each series, show good ligand efficiency. We propose a route for their further development into potent and selective inhibitors of METTL3.


  • Organizational Affiliation

    Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N6-adenosine-methyltransferase catalytic subunit580Homo 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 subunit456Homo 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
NXB (Subject of Investigation/LOI)
Query on NXB

Download Ideal Coordinates CCD File 
C [auth A](2~{R},3~{R},4~{R},5~{R})-2-[(6-aminopurin-9-yl)methyl]-5-azanyl-oxane-3,4-diol
C11 H16 N6 O3
YFNWLMALNRKCLH-GCXDCGAKSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.21α = 90
b = 64.21β = 90
c = 226.57γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030B_189363

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description