9D12: Smarca2 Bromodomain

Smarca2 Bromodomain in complex with compound 15. Determined by X-ray diffraction at 2.1 Å resolution. Released 15 Jan 2025.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,919
Mol. weight: 44.94 kDa
Ligands: A1A1P, ZN
Released: 15 Jan 2025

Explore 9D12 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D12 contains 24 α-helices and 6 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1382-1396	15
β-strand	1398	1	1
β-strand	1404	1	1
α-helix	1405-1409	5
α-helix	1412-1414	3
α-helix	1419-1424	6
α-helix	1431-1439	9
α-helix	1446-1463	18
α-helix	1465	1
α-helix	1469-1488	20

Chain B: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1382-1396	15
β-strand	1398	1	2
β-strand	1404	1	2
α-helix	1407-1409	3
α-helix	1412-1414	3
α-helix	1419-1424	6
α-helix	1431-1439	9
α-helix	1446-1463	18
α-helix	1465	1
α-helix	1469-1488	20

Chain C: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1384-1395	12
β-strand	1398	1	3
β-strand	1404	1	3
α-helix	1407-1409	3
α-helix	1412-1414	3
α-helix	1421-1424	4
α-helix	1431-1439	9
α-helix	1446-1463	18
α-helix	1465	1
α-helix	1469-1487	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform Short of Probable global transcription activator SNF2L2	A, B, C	protein	124	Homo sapiens	P51531 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>9D12_1 Isoform Short of Probable global transcription activator SNF2L2 (chains A, B, C)
SNAAEKLSPNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELPEYYELIRKPV
DFKKIKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSARQKIA
KEEE

Ligands and cofactors

ID	Name	Formula	Copies
A1A1P	(12'R)-4'-chloro-9'-(piperidin-4-yl)-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]qu…	C25 H26 Cl N3 O	3
ZN	Zinc ion	Zn	3

Water and common crystallization additives (ACT) are not listed.

Primary citation

Discovery of High-Affinity SMARCA2/4 Bromodomain Ligands and Development of Potent and Exceptionally Selective SMARCA2 PROTAC Degraders. Leng, L., Tu, W., Yang, L. et al. J Med Chem (2025) 68:1113-1133. DOI 10.1021/acs.jmedchem.4c01903 · PubMed

Other PDB entries of the same protein (UniProt P51531 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6HAZ 1.31 Å, Crystal structure of the bromodomain of human SMARCA2 in complex with SMARCA-BD ligand
7Z76 1.32 Å, Crystal structure of compound 10 in complex with the bromodomain of human SMARCA2 and…
7Z78 1.32 Å, Crystal structure of compound 4 in complex with the bromodomain of human SMARCA2 and…
5DKC 1.6 Å, Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with PFI-3…
9D11 1.68 Å, Smarca2 Bromodomain in complex with compound 22
5DKH 1.7 Å, Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with a…
9E30 1.71 Å, Discovery of Potent, Highly Selective and Efficacious SMARCA2 Degraders - Compound 13
9E31 1.96 Å, Discovery of Potent, Highly Selective and Efficacious SMARCA2 Degraders - Compound 6
4QY4 1.97 Å, Crystal structure of the bromodomain of human SMARCA2
7Z77 1.97 Å, Crystal structure of compound 6 in complex with the bromodomain of human SMARCA2 and…
9QAC 2.07 Å, Crystal structure of the SMARCA2 bromodomain bound to a fragment screening hit
9QAD 2.08 Å, Crystal structure of the SMARCA2 bromodomain bound to a tricyclic pyrimidoindolone…

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