6TTV

Crystal structure of the human METTL3-METTL14 complex bound to Compound 3 (ASI_M3M_138)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1002/cmdc.202000011
  • Primary Citation of Related Structures:  
    6Y4G, 6TTP, 6TU1, 6TTT, 6TTW, 6TTV, 6TTX

  • 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N6-adenosine-methyltransferase catalytic subunit A580Homo sapiensMutation(s): 0 
Gene Names: METTL3, MTA70
EC: 2.1.1.348
Find proteins for Q86U44 (Homo sapiens)
Explore Q86U44 
Go to UniProtKB:  Q86U44
NIH Common Fund Data Resources
PHAROS:  Q86U44
GTEx:  ENSG00000165819
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
N6-adenosine-methyltransferase non-catalytic subunit B456Homo sapiensMutation(s): 0 
Gene Names: METTL14, KIAA1627
Find proteins for Q9HCE5 (Homo sapiens)
Explore Q9HCE5 
Go to UniProtKB:  Q9HCE5
NIH Common Fund Data Resources
PHAROS:  Q9HCE5
GTEx:  ENSG00000145388
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NWW
Query on NWW
Download Ideal Coordinates CCD File 
A
(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolane-2-carboxamide
C10 H12 N6 O4
BLMHAOGGJQDPLX-LKCKTBJASA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.15α = 90
b = 64.15β = 90
c = 225.4γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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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