7O2F | pdb_00007o2f

Crystal structure of the human METTL3-METTL14 complex bound to Compound 22 (UZH2)

• PDB DOI: https://doi.org/10.2210/pdb7O2F/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2021-03-30 Released: 2021-09-01 
• Deposition Author(s): Bedi, R.K., Dolbois, A., Caflisch, A.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.242 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

1,4,9-Triazaspiro[5.5]undecan-2-one Derivatives as Potent and Selective METTL3 Inhibitors.

Dolbois, A., Bedi, R.K., Bochenkova, E., Muller, A., Moroz-Omori, E.V., Huang, D., Caflisch, A.

(2021) J Med Chem 64: 12738-12760

• PubMed: 34431664 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c00773
• Primary Citation Related Structures: 
  7O08, 7O09, 7O0L, 7O29, 7O2E, 7O2F


• PubMed Abstract: 
  

  N ⁶ -methyladenosine (m ⁶ A) is the most frequent of the 160 RNA modifications reported so far. Accumulating evidence suggests that the METTL3/METTL14 protein complex, part of the m ⁶ A regulation machinery, is a key player in a variety of diseases including several types of cancer, type 2 diabetes, and viral infections. Here we report on a protein crystallography-based medicinal chemistry optimization of a METTL3 hit compound that has resulted in a 1400-fold potency improvement (IC ₅₀ of 5 nM for the lead compound 22 ( UZH2 ) in a time-resolved Förster resonance energy transfer (TR-FRET) assay). The series has favorable ADME properties as physicochemical characteristics were taken into account during hit optimization. UZH2 shows target engagement in cells and is able to reduce the m ⁶ A/A level of polyadenylated RNA in MOLM-13 (acute myeloid leukemia) and PC-3 (prostate cancer) cell lines.

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Organizational Affiliation: 
• Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.34 kDa 
• Atom Count: 3,722 
• Modeled Residue Count: 447 
• Deposited Residue Count: 536 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N6-adenosine-methyltransferase catalytic subunit	A	246	Homo sapiens	Mutation(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 GTEx:  ENSG00000165819

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N6-adenosine-methyltransferase non-catalytic subunit	B	290	Homo sapiens	Mutation(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 GTEx:  ENSG00000145388

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UZ5 (Subject of Investigation/LOI)	C [auth A]	4-[4-[(4,4-dimethylpiperidin-1-yl)methyl]-2,5-bis(fluoranyl)phenyl]-9-[6-(methylamino)pyrimidin-4-yl]-1,4,9-triazaspiro[5.5]undecan-2-one C27 H37 F2 N7 O GYWOVBUGFWWSJR-UHFFFAOYSA-N
ACT	D [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
UZ5	BindingDB:  7O2F	IC50: min: 5, max: 8 (nM) from 2 assay(s)
		EC50: min: 850, max: 2000 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.242 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.25	α = 90
b = 64.25	β = 90
c = 225.77	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-01 
Deposition Author(s): Bedi, R.K., Dolbois, A., Caflisch, A.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030B_189363

Revision History  

• Version 1.0: 2021-09-01
  Type: Initial release
  
• Version 1.1: 2021-09-15
  Changes: Database references
• Version 1.2: 2021-09-22
  Changes: Data collection, Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary