9G4S | pdb_00009g4s

Crystal structure of the human METTL3-METTL14 in complex with small molecule inhibitor Compound 56

PDB DOI: https://doi.org/10.2210/pdb9G4S/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-07-16 Released: 2025-02-12
Deposition Author(s): Dutheuil, G., Oukoloff, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.243 (Depositor), 0.248 (DCC)
R-Value Work:
0.195 (Depositor), 0.203 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Discovery, Optimization, and Preclinical Pharmacology of EP652, a METTL3 Inhibitor with Efficacy in Liquid and Solid Tumor Models.

Dutheuil, G., Oukoloff, K., Korac, J., Lenoir, F., El Bousmaqui, M., Probst, N., Lapin, A., Nakhabina, G., Sorlet, C., Parmentier, N., Karila, D., Ghavtadze, N., Casault, P., Claridge, S., Sapmaz, S., Slater, M.J., Fraser, G.L.

(2025) J Med Chem 68: 2981-3003

PubMed: 39883878 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.4c02225
Primary Citation of Related Structures:
9G4S, 9G4U, 9G4W

PubMed Abstract:
METTL3 is the RNA methyltransferase predominantly responsible for the addition of N ⁶-methyladenosine (m ⁶A), the most abundant modification to mRNA. The prevalence of m ⁶A and the activity and expression of METTL3 have been linked to the appearance and progression of acute myeloid leukemia (AML), thereby making METTL3 an attractive target for cancer therapeutics. We report herein the discovery and optimization of small-molecule inhibitors of METTL3, culminating in the selection of EP652 as an in vivo proof-of-concept compound. EP652 potently inhibits the enzymatic activity of METTL3, has favorable PK parameters, and demonstrates efficacy in preclinical oncology models, indicating that pharmacological inhibition of METTL3 is a viable strategy for the treatment of liquid and solid tumors.

Organizational Affiliation

Epics Therapeutics SA, rue Adrienne Bolland 47, Gosselies 6041, Belgium.

Macromolecule Content

Total Structure Weight: 57.98 kDa
Atom Count: 4,256
Modeled Residue Count: 468
Deposited Residue Count: 494
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N6-adenosine-methyltransferase catalytic subunit	A	214	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q86U44
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N6-adenosine-methyltransferase non-catalytic subunit	B	280	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HCE5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1III Query on A1III Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-[(3~{R})-3-(cyclopropylmethylamino)piperidin-1-yl]-1-[(1~{R})-1-[4-[5-(dimethylamino)pyridin-3-yl]-1,2,3-triazol-1-yl]ethyl]pyridin-2-one C₂₅ H₃₄ N₈ O SIMGHJKPZKGPGZ-WIYYLYMNSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]