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)

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Ligand Structure Quality Assessment

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

Literature

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

Alford, J., Farrow, N.A.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P51531
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
A1AHQ (Subject of Investigation/LOI) Query on A1AHQ Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	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		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History (Full details and data files)

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

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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.