7ACD

Crystal structure of the human METTL3-METTL14 complex with compound T30 (UZH1a)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history. 


Literature

METTL3 Inhibitors for Epitranscriptomic Modulation of Cellular Processes.

Moroz-Omori, E.V., Huang, D., Kumar Bedi, R., Cheriyamkunnel, S.J., Bochenkova, E., Dolbois, A., Rzeczkowski, M.D., Li, Y., Wiedmer, L., Caflisch, A.

(2021) ChemMedChem 16: 3035-3043

  • DOI: 10.1002/cmdc.202100291
  • Primary Citation of Related Structures:  
    7ACD

  • PubMed Abstract: 

    • The methylase METTL3 is the writer enzyme of the N 6 -methyladenosine (m 6 A) modification of RNA. Using a structure-based drug discovery approach, we identified a METTL3 inhibitor with potency in a biochemical assay of 280 nM, while its enantiomer is 100 times less active ...

    The methylase METTL3 is the writer enzyme of the N 6 -methyladenosine (m 6 A) modification of RNA. Using a structure-based drug discovery approach, we identified a METTL3 inhibitor with potency in a biochemical assay of 280 nM, while its enantiomer is 100 times less active. We observed a dose-dependent reduction in the m 6 A methylation level of mRNA in several cell lines treated with the inhibitor already after 16 h of treatment, which lasted for at least 6 days. Importantly, the prolonged incubation (up to 6 days) with the METTL3 inhibitor did not alter levels of other RNA modifications (i. e., m 1 A, m 6 A m , m 7 G), suggesting selectivity of the developed compound towards other RNA methyltransferases.

    Related Citations: 
    • METTL3 inhibitors for epitranscriptomic modulation of cellular processes
      Moroz-Omori, E.V., Huang, D., Bedi, R.K., Cheriyamkunnel, S.J., Bochenkova, E., Dolbois, A., Rzeczkowski, M.D., Wiedmer, L., Caflisch, A.
      (2020) Biorxiv --: --
    • Structural and Dynamic Insights into Redundant Function of YTHDF Proteins.
      Li, Y., Bedi, R.K., Moroz-Omori, E.V., Caflisch, A.
      (2020) J Chem Inf Model --: --
    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N6-adenosine-methyltransferase catalytic subunitA246Homo sapiensMutation(s): 0 
Gene Names: METTL3, MTA70
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86U44
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
N6-adenosine-methyltransferase non-catalytic subunitB290Homo sapiensMutation(s): 0 
Gene Names: METTL14, KIAA1627
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCE5 (Homo sapiens)
Explore Q9HCE5 
Go to UniProtKB:  Q9HCE5
PHAROS:  Q9HCE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HCE5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R72 (Subject of Investigation/LOI)
Query on R72
Download Ideal Coordinates CCD File 
C [auth A]4-[(4,4-dimethylpiperidin-1-yl)methyl]-2-oxidanyl-~{N}-[[(3~{R})-3-oxidanyl-1-[6-[(phenylmethyl)amino]pyrimidin-4-yl]piperidin-3-yl]methyl]benzamide
C32 H42 N6 O3
PWYRDVXYAOGDNK-JGCGQSQUSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
E [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.8α = 90
b = 63.8β = 90
c = 224.92γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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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: 2020-10-28
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2020-11-11
    Changes: Database references
  • Version 2.0: 2021-03-24
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2021-07-21
    Changes: Database references
  • Version 2.2: 2021-10-13
    Changes: Data collection, Database references