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)

---

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

Structure-Activity relationship studies of SETD8 covalent inhibitors

Ma, A., Babault, N., Hong, W., Dong, A., Hong, Z., Xin, C., Park, K.S., Brown, P.J., Liu, J., Vedadi, M., Jin, J.

To be published.

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.

---

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