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)

wwPDB Validation 3D Report Full Report

Validation slider image for 9CR7

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NQR1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E1J Query on E1J Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
H81 (Subject of Investigation/LOI) Query on H81 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	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		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-30

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-07-30
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.