9CR7 | pdb_00009cr7

Structure of human SETD8 in complex with covalent inhibitor AM2928

• PDB DOI: https://doi.org/10.2210/pdb9CR7/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-20 Released: 2025-07-30 
• Deposition Author(s): Babault, N., Park, K.S., Jin, J.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.233 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Discovery of a Potent, Selective, and In Vivo Efficacious Covalent Inhibitor for Lysine Methyltransferase SETD8.

Chen, H., Dutta, R.P., Li, Z., Zhong, Y., Ma, A., Park, K.S., Kottur, J., Park, A., Babault, N., Wang, K., Wang, D., Xiong, Y., Kaniskan, H.U., Luo, M., Parekh, S., Jin, J.

(2026) J Med Chem 69: 4255-4269

• PubMed: 41693203 
• DOI: https://doi.org/10.1021/acs.jmedchem.5c02958
• Primary Citation Related Structures: 
  9CR7


• PubMed Abstract: 
  

  Dysregulated signaling of SET domain-containing protein 8 (SETD8) has been implicated in tumorigenesis, yet most SETD8 inhibitors exhibited limited cellular efficacy. Herein, we developed a potent and selective SETD8 covalent inhibitor, MS2928 ( 3 ), featuring a propiolamide covalent warhead. Compound 3 potently and selectively inhibited SETD8 methyltransferase activity. The covalent inhibition mechanism of 3 was confirmed by mass spectrometry and X-ray crystallography. Moreover, 3 significantly reduced the histone H4 lysine 20 monomethylation (H4K20me1) levels in cells and robustly inhibited the proliferation of SETD8-overexpressing multiple myeloma (MM) cell lines with no significant antiproliferative effect on SETD8-low expressing MM cells and normal cells. Importantly, 3 effectively inhibited tumor growth in vivo in two xenograft mouse models of SETD8-overexpressing MM cell lines. Collectively, our results establish 3 as a valuable chemical tool for exploring the biological functions of SETD8 and pave the way for further development of novel epigenetic therapies for MM.

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Organizational Affiliation: 
• Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States.
Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, The Precision Immunology Institute at Mount Sinai, New York, New York 10029, United States.
Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States.
Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, New York 10021, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.34 kDa 
• Atom Count: 2,399 
• Modeled Residue Count: 285 
• Deposited Residue Count: 352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-lysine methyltransferase KMT5A	A, B	176	Homo sapiens	Mutation(s): 0  Gene Names: KMT5A, PRSET7, SET07, SET8, SETD8 EC: 2.1.1 (PDB Primary Data), 2.1.1.361 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQR1 (Homo sapiens) Explore Q9NQR1  Go to UniProtKB:  Q9NQR1
PHAROS:  Q9NQR1 GTEx:  ENSG00000183955

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E1J	C [auth A]	N-(3-{[7-(2-aminoethoxy)-6-methoxy-2-(pyrrolidin-1-yl)quinazolin-4-yl]amino}propyl)prop-2-enamide C21 H30 N6 O3 WNUZMICKSFVTAC-UHFFFAOYSA-N
H81 (Subject of Investigation/LOI)	D [auth B]	N-(3-{[7-(2-aminoethoxy)-6-methoxy-2-(pyrrolidin-1-yl)quinazolin-4-yl]amino}propyl)prop-2-ynamide C21 H28 N6 O3 OTBDPSSADBTPAB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.233 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.715	α = 90
b = 102.457	β = 90
c = 110.713	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Babault, N., Park, K.S., Jin, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01GM122749

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release
  
• Version 1.1: 2026-08-12
  Changes: Database references