9MRE | pdb_00009mre

From DNA-Encoded Library Screening to AM-9747 - an MTA-Cooperative PRMT5 Inhibitor with Potent Oral in vivo Efficacy

PDB DOI: https://doi.org/10.2210/pdb9MRE/pdb

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

Deposited: 2025-01-07 Released: 2025-03-26
Deposition Author(s): GhimireRijal, S., Mukund, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.241 (Depositor), 0.246 (DCC)
R-Value Work:
0.202 (Depositor), 0.211 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

From DNA-Encoded Library Screening to AM-9747 : An MTA-Cooperative PRMT5 Inhibitor with Potent Oral In Vivo Efficacy.

Sarvary, I., Vestergaard, M., Moretti, L., Andersson, J., Peiro Cadahia, J., Cowland, S., Flagstad, T., Franch, T., Gouliaev, A., Husemoen, G., Jacso, T., Kronborg, T., Kuropatnicka, A., Nadali, A., Madsen, M., Nielsen, S.R., Pii, D., Ryborg, S.R., Soede, C., Allen, J.R., Bourbeau, M., Li, K., Liu, Q., Lo, M.C., Madoux, F., Mardirossian, N., Moriguchi, J., Ngo, R., Peng, C.C., Pettus, L., Tamayo, N., Wang, P., Kapoor, R., Belmontes, B., Caenepeel, S., Hughes, P., Liu, S., Slemmons, K.K., Yang, Y., Xie, F., Ghimire-Rijal, S., Mukund, S., Glad, S.

(2025) J Med Chem 68: 6534-6557

PubMed: 40102181 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.4c03101
Primary Citation Related Structures:
9MRE

PubMed Abstract:
Inhibition of the methyltransferase enzyme PRMT5 by MTA accumulation is a vulnerability of MTAP-deleted cancers. Herein, we report the discovery and optimization of a quinolin-2-amine DEL hit that cooperatively binds PRMT5:MEP50 and MTA to generate a catalytically inhibited ternary complex. X-ray crystallography confirms quinolin-2-amine binding of PRMT5 glutamate-444, while simultaneously exhibiting a hydrophobic interaction with MTA. Lead optimization produced AM-9747 , which selectively inhibits PRMT5-directed symmetric dimethylation of arginine residues of proteins, leading to a potent reduction of cell viability in MTAP-del cells compared to MTAP-WT cells. Once-daily oral dosing of AM-9747 in mouse xenografts is well tolerated, displaying a robust and dose-dependent inhibition of symmetric dimethylation of arginine in MTAP-del tumor-xenografts and significant concomitant tumor growth inhibition without any significant effect on MTAP-WT tumor xenografts.

Organizational Affiliation

Amgen Research, Amgen Inc, Ro̷nnegade 8, DK-2100 Copenhagen, Denmark.

Macromolecule Content

Total Structure Weight: 112.94 kDa
Atom Count: 7,942
Modeled Residue Count: 933
Deposited Residue Count: 994
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 5	A	650	Homo sapiens	Mutation(s): 0 Gene Names: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 EC: 2.1.1.320
UniProt & NIH Common Fund Data Resources
Find proteins for O14744 (Homo sapiens) Explore O14744 Go to UniProtKB: O14744
PHAROS: O14744 GTEx: ENSG00000100462
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O14744
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylosome protein 50	B	344	Homo sapiens	Mutation(s): 0 Gene Names: WDR77, MEP50, WD45, HKMT1069, Nbla10071
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQA1 (Homo sapiens) Explore Q9BQA1 Go to UniProtKB: Q9BQA1
PHAROS: Q9BQA1 GTEx: ENSG00000116455
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BQA1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BQW (Subject of Investigation/LOI) Query on A1BQW 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]	2-amino-3-methyl-N-[(1R)-1-(pyrimidin-2-yl)ethyl]-N-{[5-(trifluoromethyl)pyridin-2-yl]methyl}quinoline-6-carboxamide C₂₄ H₂₁ F₃ N₆ O QRZCNKOBDDQUAP-OAHLLOKOSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MTA Query on MTA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	5'-DEOXY-5'-METHYLTHIOADENOSINE C₁₁ H₁₅ N₅ O₃ S WUUGFSXJNOTRMR-IOSLPCCCSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B]	H [auth A], K [auth A], N [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth A] Focus chain N [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain M [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth A] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A], I [auth A], M [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain M [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain M [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B]	J [auth A], L [auth A], O [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth A] Focus chain O [auth B] Interactions & Density Focus chain J [auth A] Focus chain L [auth A] Focus chain O [auth B]