9AYQ | pdb_00009ayq

SMARCA2 in complex with a pyridine-2-one-based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9AYQ/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Baculovirus expression vector pFastBac1-HM
• Mutation(s): No 


• Deposited: 2024-03-08 Released: 2025-04-09 
• Deposition Author(s): Farrow, N.A., Cocozaki, A.
• Funding Organization(s): Other private

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.287 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Literature

Discovery of a SMARCA2/4 ATPase Inhibitors Suitable for Use in SMARCA4-mutant Preclinical Models

Alford, J., Farrow, N.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 163.42 kDa 
• Atom Count: 9,634 
• Modeled Residue Count: 1,152 
• Deposited Residue Count: 1,386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable global transcription activator SNF2L2	A, B	693	Homo sapiens	Mutation(s): 0  Gene Names: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P51531 (Homo sapiens) Explore P51531  Go to UniProtKB:  P51531
PHAROS:  P51531 GTEx:  ENSG00000080503

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], E [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
A1AHQ (Subject of Investigation/LOI)	D [auth A], F [auth B]	4-cyano-N-[1-(2,2-difluoroethyl)-5-fluoro-6-oxo-1,6-dihydropyridin-3-yl]-5-(trifluoromethyl)thiophene-2-carboxamide C14 H7 F6 N3 O2 S BBVUKPZENMWLFA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.287 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.106	α = 90
b = 63.967	β = 102.18
c = 126.575	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Farrow, N.A., Cocozaki, A.

---

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release