9PKU | pdb_00009pku

Crystal Structure of YEATS domain of human YEATS2 in complex with LS-131 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 
    0.251 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Complex-specific inhibitors for interrogating ATAC histone acetyltransferase complex.

Liu, S.Liu, J.Wu, Y.Yao, X.Li, X.Dong, X.Li, Q.Cheung, H.J.H.Wong, K.Y.Li, Y.He, M.Chiang, C.L.Wong, J.W.H.Li, H.Wang, W.Li, X.Li, X.D.

(2026) Nat Chem Biol 22: 471-481

  • DOI: https://doi.org/10.1038/s41589-025-02132-7
  • Primary Citation Related Structures: 
    9PKU

  • PubMed Abstract: 

    Histone acetyltransferases (HATs) modify chromatin to regulate gene expression. Instead of acting alone, HATs function in complexes with other proteins, leading to variations in substrate specificity, genomic localization and cellular function. To understand the complex-dependent roles of HATs, we present a chemical approach to specifically dissociate ATAC (Ada-two-A-containing) HAT complex from chromatin without perturbing other complexes. Rather than targeting the shared HAT enzyme, we developed chemical inhibitors for an ATAC-specific subunit, YEATS2. The most effective inhibitor, LS-170, specifically reduced the chromatin occupancy of the ATAC complex, decreased the ATAC-dependent histone acetylation level and downregulated the expression of ATAC-governed genes, leading to significantly suppressed tumor growth in a lung cancer mouse model. This study not only sheds light on the regulatory roles of the ATAC HAT complex in gene transcription but also provides evidence that the chemical inhibition of the ATAC complex can be a promising therapeutic strategy.


  • Organizational Affiliation
    • Department of Chemistry, The University of Hong Kong, Hong Kong, China.

Macromolecule Content 

  • Total Structure Weight: 34.3 kDa 
  • Atom Count: 2,435 
  • Modeled Residue Count: 275 
  • Deposited Residue Count: 280 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
YEATS domain-containing protein 2
A, C
135Homo sapiensMutation(s): 0 
Gene Names: YEATS2KIAA1197
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULM3 (Homo sapiens)
Explore Q9ULM3 
Go to UniProtKB:  Q9ULM3
PHAROS:  Q9ULM3
GTEx:  ENSG00000163872 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ULM3
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
LS-131 peptide
B, D
5Homo sapiensMutation(s): 0 
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BZ2
(Subject of Investigation/LOI)

Query on BZ2



Download:Ideal Coordinates CCD File
H [auth B],
Q [auth D]
1-benzofuran-2-carboxylic acid
C9 H6 O3
OFFSPAZVIVZPHU-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
L [auth C]
M [auth C]
E [auth A],
F [auth A],
G [auth A],
L [auth C],
M [auth C],
N [auth C],
O [auth C],
P [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth C],
J [auth C],
K [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
A1EDD
Query on A1EDD
B, D
D-PEPTIDE LINKINGC7 H16 N2 O4 SDLY

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free:  0.251 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.399α = 90
b = 51.559β = 93.93
c = 54.381γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China2242500053

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-07
    Type: Initial release
  • Version 1.1: 2026-07-22
    Changes: Database references