9NWY | pdb_00009nwy

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

• PDB DOI: https://doi.org/10.2210/pdb9NWY/pdb

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


• Deposited: 2025-03-24 Released: 2025-05-07 
• Deposition Author(s): GhimireRijal, S., Mukund, S.
• Funding Organization(s): Not funded

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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

Literature

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

Anderson, J., Cowland, S., Vestergaard, M., Yang, Y., Liu, S., Fang, X., Mukund, S., GhimireRijal, S., Carter, C., Jasco, T., Savary, I., Hughes, P.E., Gouliaev, A., Belmontes, B., Caenepeel, S., Franch, T., Glad, S., Husemoen, B., Nielson, S.J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

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

Macromolecules

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 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1B6Y (Subject of Investigation/LOI)	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	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 = 104.261	α = 90
b = 138.384	β = 90
c = 178.425	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-07 
Deposition Author(s): GhimireRijal, S., Mukund, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-05-07
  Type: Initial release