9KLA | pdb_00009kla

Crystal Structure of the bromodomain of human BRD9 in complex with the inhibitor Y22024

• PDB DOI: https://doi.org/10.2210/pdb9KLA/pdb

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


• Deposited: 2024-11-14 Released: 2025-11-05 
• Deposition Author(s): Chen, Z., Zhang, C., Xu, H., Wu, X., Zhang, Y., Xu, Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Key imidazolyl groups that induce phenylalanine flipping enhance the efficacy of oral BRD9 inhibitors for AML treatment

Chen, Z., Zhang, C., Shen, H., Xu, H., Huang, Y., Dong, R., Tang, X., Chai, S., Li, J., Xu, J., Zhang, X., Zhang, Y., Wu, X., Xu, Y.

(2025) Acta Pharm Sin B 

• DOI: https://doi.org/10.1016/j.apsb.2025.08.006

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.25 kDa 
• Atom Count: 1,246 
• Modeled Residue Count: 131 
• Deposited Residue Count: 149 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 9	A	149	Homo sapiens	Mutation(s): 0  Gene Names: BRD9, UNQ3040/PRO9856
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H8M2 (Homo sapiens) Explore Q9H8M2  Go to UniProtKB:  Q9H8M2
PHAROS:  Q9H8M2 GTEx:  ENSG00000028310

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EF0	B [auth A], E [auth A]	1-[1-(3,5-dimethoxyphenyl)indolizin-3-yl]ethanone C18 H17 N O3 FTNILURDQGAJNO-UHFFFAOYSA-N
MLT	D [auth A]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.22	α = 90
b = 58.22	β = 90
c = 87.384	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Chen, Z., Zhang, C., Xu, H., Wu, X., Zhang, Y., Xu, Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2022YFE0210600

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release