9MGN image
Entry Detail
PDB ID:
9MGN
Title:
Crystal structure of PRMT5:MEP50 in complex with MTA and compound 41
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2024-12-11
Release Date:
2025-03-05
Method Details:
Experimental Method:
Resolution:
2.82 Å
R-Value Free:
0.28
R-Value Work:
0.22
R-Value Observed:
0.23
Space Group:
I 2 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Protein arginine N-methyltransferase 5
Chain IDs:A
Chain Length:645
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Methylosome protein 50
Chain IDs:B
Chain Length:350
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
MTA-Cooperative PRMT5 Inhibitors: Mechanism Switching Through Structure-Based Design.
J.Med.Chem. 68 4217 4236 (2025)
PMID: 39919252 DOI: 10.1021/acs.jmedchem.4c01998

Abstact

Deletion of the MTAP gene leads to accumulation of the substrate of the MTAP protein, methylthioadenosine (MTA). MTA binds PRMT5 competitively with S-adenosyl-l-methionine (SAM), and selective inhibition of the PRMT5•MTA complex relative to the PRMT5•SAM complex can lead to selective killing of cancer cells with MTAP deletion. Herein, we describe the discovery of novel compounds using structure-based drug design to switch the mechanism of binding of known, SAM-cooperative PRMT5 inhibitors to an MTA-cooperative binding mechanism by occupying the portion of the SAM binding pocket in PRMT5 that is unoccupied when MTA is bound and hydrogen bonding to Arg368, thereby allowing them to selectively target MTAP-deleted cancer cells.

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Primary Citation of related structures