9D12

Smarca2 Bromodomain in complex with compound 15

PDB DOI: https://doi.org/10.2210/pdb9D12/pdb

Classification: GENE REGULATION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-08-07 Released: 2025-01-15
Deposition Author(s): Meagher, J.L., Stuckey, J.A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.240 (Depositor), 0.234 (DCC)
R-Value Work:
0.216 (Depositor), 0.207 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Discovery of High-Affinity SMARCA2/4 Bromodomain Ligands and Development of Potent and Exceptionally Selective SMARCA2 PROTAC Degraders.

Leng, L., Tu, W., Yang, L., Huang, L., Wang, M., Meagher, J.L., Chinnaswamy, K., Allu, S.R., Rej, R.K., Tosovic, J., Harikrishnan, L., Li, Z., Sui, Z., Stuckey, J.A., Wang, S.

(2025) J Med Chem 68: 1113-1133

PubMed: 39745064 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.4c01903
Primary Citation of Related Structures:
9D11, 9D12

PubMed Abstract:
In the SWI/SNF chromatin-remodeling complex, the mutually exclusive catalytic ATPase subunits SMARCA2 and SMARCA4 proteins have a synthetic-lethal relationship. Selectively targeting SMARCA2 for degradation is a promising and new therapeutic strategy for human cancers harboring inactivated mutated SMARCA4. In this study, we report the design, synthesis, and biological evaluation of novel SMARCA2/4 ligands and our subsequent design of PROTAC degraders using high-affinity SMARCA ligands and VHL-1 ligands. Our efforts led to the discovery of high-affinity SMARCA2/4 bromodomain ligands and the development of a potent and selective SMARCA2 degrader and a highly potent SMARCA2/4 and PBRM1 degrader.

Organizational Affiliation

Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States.

Macromolecule Content

Total Structure Weight: 44.94 kDa
Atom Count: 2,919
Modelled Residue Count: 326
Deposited Residue Count: 372
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform Short of Probable global transcription activator SNF2L2	A, B, C	124	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51531
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A1P (Subject of Investigation/LOI) Query on A1A1P Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C]	E [auth A], I [auth B], L [auth C]	(12'R)-4'-chloro-9'-(piperidin-4-yl)-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-5'-one C₂₅ H₂₆ Cl N₃ O MEFDDENEEVLEBY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C]	D [auth A], H [auth B], K [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain K [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	F [auth A], G [auth A], J [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B]