9F0A | pdb_00009f0a

N5 Adduct of LSD1-CoREST in complex with MC4455

• PDB DOI: https://doi.org/10.2210/pdb9F0A/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-15 Released: 2025-04-23 
• Deposition Author(s): Barone, M., Mattevi, A.
• Funding Organization(s): Italian Ministry of Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.36 Å
• R-Value Free: 
  0.234 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

A synergistic interaction between PRMT5 and LSD1 inhibitors in AML.

Param, N.J., Arceci, E., Fiorentino, F., Pignata, L., Torre, D., Gutierrez-Trejo, N., Fong, J.Y., Goy, P.A., Han, B.Y., Lambona, C., Di Bello, E., Castiello, C., Barone, M., Schwarz, M., Arrowsmith, C., Ito, K., Scherle, P., Wee, D.K.B., Ndoye, S., Tabaglio, T., Jeyasekharan, A.D., Lakshmanan, M., Cirilli, R., Habisch, H., Madl, T., Mattevi, A., Valente, S., Mai, A., Guccione, E.

(2026) Sci Adv 12: eaea4059-eaea4059

• PubMed: 41894488 
• DOI: https://doi.org/10.1126/sciadv.aea4059
• Primary Citation Related Structures: 
  9F0A


• PubMed Abstract: 
  

  Acute myeloid leukemia (AML) is a hematopoietic malignancy caused by abnormal proliferation and differentiation of blasts. PRMT5, a methyltransferase that catalyzes symmetric dimethylation of arginine (SDMA) residues, has been implicated in cancer stem cell homeostasis and shown to be a potential therapeutic target in AML. However, given the toxicity of complete PRMT5 inhibition, there is a need to identify effective synergistic therapies. Through a targeted screen of compounds that inhibit key nodes of PRMT5-regulated pathways, we identified a synthetic lethality between inhibition of PRMT5 and LSD1, a lysine demethylase known to affect AML blast differentiation. The two inhibitors broadly reshape the transcriptome of targeted cells and synergize to promote AML differentiation and eventually growth inhibition and apoptosis, in a p53-dependent manner. To leverage this synthetic lethal interaction, we generated new dual compounds to inhibit both enzymes and recapitulated the effects of the drug combination. Our results uncover an unexpected convergence of PRMT5- and LSD1-regulated targets, paving the way for new therapeutic opportunities.

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Organizational Affiliation: 
• Center for OncoGenomics and Innovative Therapeutics (COGIT); Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, NY, New York, USA.
Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy.
Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy.
Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore.
Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore.
Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
SGC Toronto, Toronto, Canada.
Prelude Therapeutics, Wilmington, DE, USA.
Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
Department of Haematology-Oncology, National University Hospital, Singapore, Singapore.
Centre for the Control and Evaluation of Medicines, Chemical Medicines Unit, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria.
BioTechMed-Graz, Graz, Austria.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 102.77 kDa 
• Atom Count: 6,380 
• Modeled Residue Count: 799 
• Deposited Residue Count: 908 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific histone demethylase 1A	A	730	Homo sapiens	Mutation(s): 0  Gene Names: KDM1A, AOF2, KDM1, KIAA0601, LSD1 EC: 1 (PDB Primary Data), 1.14.11 (UniProt), 1.14.99.66 (UniProt), 1.14.11.65 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60341 (Homo sapiens) Explore O60341  Go to UniProtKB:  O60341
PHAROS:  O60341 GTEx:  ENSG00000004487

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REST corepressor 1	B	178	Homo sapiens	Mutation(s): 0  Gene Names: RCOR1, KIAA0071, RCOR
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKL0 (Homo sapiens) Explore Q9UKL0  Go to UniProtKB:  Q9UKL0
PHAROS:  Q9UKL0 GTEx:  ENSG00000089902

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1H8N (Subject of Investigation/LOI)	C [auth A]	[[(2~{S},3~{R},4~{S},5~{S})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{S},3~{S},4~{R})-5-[5-[3-[4-[[4-[[(2~{S})-3-(3,4-dihydro-1~{H}-isoquinolin-2-yl)-2-oxidanyl-propyl]carbamoyl]pyridin-2-yl]amino]phenyl]propanoyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-4~{a}~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate C54 H63 N13 O18 P2 XWHWYVHMOOWMKZ-MBYMQWEBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.36 Å
• R-Value Free:  0.234 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.438	α = 90
b = 179.767	β = 90
c = 234.461	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-23 
Deposition Author(s): Barone, M., Mattevi, A.

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Funding Organization	Location	Grant Number
Italian Ministry of Education	Italy	MUR project 404 FISR2019_00374 MeDyCa

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release
  
• Version 1.1: 2026-05-06
  Changes: Database references