9NWY | pdb_00009nwy

Discovery of MTA-cooperative PRMT5 Inhibitors from Co-factor directed DNA-Encoded Library Screens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.272 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

MTA-cooperative PRMT5 inhibitors from cofactor-directed DNA-encoded library screens.

Andersson, J.Cowland, S.Vestergaard, M.Yang, Y.Liu, S.Fang, X.Mukund, S.Ghimire-Rijal, S.Carter, C.Chung, G.Jacso, T.Sarvary, I.Hughes, P.E.Gouliaev, A.Payton, M.Belmontes, B.Caenepeel, S.Franch, T.Glad, S.Husemoen, B.Nielsen, S.J.

(2025) Proc Natl Acad Sci U S A 122: e2425052122-e2425052122

  • DOI: https://doi.org/10.1073/pnas.2425052122
  • Primary Citation Related Structures: 
    9NWY

  • PubMed Abstract: 

    Methylthioadenosine phosphorylase ( MTAP ) gene deletions are frequent in human cancers. Loss of MTAP leads to significantly increased cellular levels of methylthioadenosine (MTA), a cellular metabolite and specific inhibitor of the cell-essential enzyme Protein Arginine Methyltransferase-5 (PRMT5). Using a cofactor-directed screening strategy and DNA-encoded libraries, we identify a class of PRMT5 inhibitors that cooperatively inhibit PRMT5 in the presence of MTA. An optimized inhibitor, AM-9934, selectively inhibits PRMT5 in MTAP -deleted cells and in transplanted tumors while sparing MTAP -expressing counterparts, leading to specific suppression of viability in MTAP -deleted cells. Structural studies show that AM-9934 occupies the arginine substrate pocket of MTA-bound PRMT5. This study introduces a broadly applicable method for directed DNA-encoded library screening toward a desired mechanistic outcome and highlights MTA-selective PRMT5 inhibition as an attractive therapeutic strategy with a potentially broad therapeutic index in patients with MTAP -deleted cancers.


  • Organizational Affiliation
    • Amgen Research, Copenhagen DK-2100, Denmark.

Macromolecule Content 

  • Total Structure Weight: 111.88 kDa 
  • Atom Count: 7,418 
  • Modeled Residue Count: 929 
  • Deposited Residue Count: 994 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 5650Homo sapiensMutation(s): 0 
Gene Names: PRMT5HRMT1L5IBP72JBP1SKB1
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14744
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Methylosome protein 50344Homo sapiensMutation(s): 0 
Gene Names: WDR77MEP50WD45HKMT1069Nbla10071
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BQA1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1B6Y
(Subject of Investigation/LOI)

Query on A1B6Y



Download:Ideal Coordinates CCD File
C [auth A]2-amino-3-methyl-N-(2-methylpropyl)-N-{[5-(trifluoromethyl)pyridin-2-yl]methyl}quinoline-6-carboxamide
C22 H23 F3 N4 O
CSGBHAZUAYOHGC-UHFFFAOYSA-N
MTA

Query on MTA



Download:Ideal Coordinates CCD File
D [auth A]5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.272 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.261α = 90
b = 138.384β = 90
c = 178.425γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Database references