9DOD | pdb_00009dod

Crystal structure of PRMT5:MEP50 in complex with PRT543

• PDB DOI: https://doi.org/10.2210/pdb9DOD/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Baculovirus expression vector pFastBac1-HM
• Mutation(s): No 


• Deposited: 2024-09-18 Released: 2025-02-12 
• Deposition Author(s): Leal, R.A., Pitis, P.M., Dou, Y., Lin, H., Wang, M., Xu, C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.259 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Phase Ib study of PRT543, an oral protein arginine methyltransferase 5 (PRMT5) inhibitor, in patients with advanced splicing factor-mutant myeloid malignancies.

Bewersdorf, J.P., Mi, X., Lu, B., Kuykendall, A., Sallman, D., Patel, M., Stevens, D., Philipovskiy, A., Sutamtewagul, G., Masarova, L., Keiffer, G., Verma, A., Bhagwat, N., Wang, M., Moore, A., Rager, J., Heiser, D., Ro, S., Hong, W.J., Abdel-Wahab, O., Stein, E.M.

(2025) Leukemia 39: 765-769

• PubMed: 39856223 
• DOI: https://doi.org/10.1038/s41375-025-02515-8
• Primary Citation of Related Structures:  
  9DOD

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Organizational Affiliation: 
• Department of Medicine; Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Yale University and Yale Cancer Center, New Haven, CT, USA.
Moffitt Cancer Center, Tampa, FL, USA.
Florida Cancer Specialists, Sarasota, FL, USA.
Norton Cancer Institute, Louisville, KY, USA.
Florida Cancer Specialists, Lake Mary, FL, USA.
University of Iowa, Iowa City, IA, USA.
MD Anderson Cancer Center, Houston, TX, USA.
Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University Hospital, Philadelphia, PA, USA.
Montefiore Einstein Comprehensive Cancer, Bronx, NY, USA.
Prelude Therapeutics, Wilmington, DE, USA.
Department of Medicine; Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA. [e-mail].
Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA. [e-mail].
Department of Medicine; Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA. [e-mail].

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: 109.94 kDa 
• Atom Count: 7,731 
• Modeled Residue Count: 938 
• Deposited Residue Count: 977 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 5	A	636	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 WDR77	B	341	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
A1A79 (Subject of Investigation/LOI)	C [auth A]	7-[(3xi,5R)-5-C-(3,4-dichlorophenyl)-3-C-methyl-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine C18 H18 Cl2 N4 O4 NVZVVFMXEHOMQR-FOOXYVKASA-N
EDO (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.259 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.567	α = 90
b = 139.202	β = 90
c = 178.548	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Leal, R.A., Pitis, P.M., Dou, Y., Lin, H., Wang, M., Xu, C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release
  
• Version 1.1: 2025-03-19
  Changes: Database references