9QAD: SMARCA2 bromodomain

Crystal structure of the SMARCA2 bromodomain bound to a tricyclic pyrimidoindolone inhibitor (compound 17). Determined by X-ray diffraction at 2.08 Å resolution. Released 14 May 2025.

Method: X-ray diffraction
Resolution: 2.08 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,907
Mol. weight: 44.21 kDa
Ligands: A1I45, ZN
Released: 14 May 2025

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

Secondary structure: helices and β-sheets

9QAD contains 26 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: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1378-1380	3
α-helix	1381-1396	16
β-strand	1398	1	1
β-strand	1422	1	1
α-helix	1423-1426	4
α-helix	1430-1432	3
α-helix	1437-1442	6
α-helix	1449-1457	9
α-helix	1464-1481	18
α-helix	1483	1
α-helix	1487-1506	20

Chain B: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1381-1396	16
β-strand	1398	1	2
β-strand	1422	1	2
α-helix	1423-1427	5
α-helix	1430-1432	3
α-helix	1437-1442	6
α-helix	1449-1457	9
α-helix	1464-1481	18
α-helix	1483	1
α-helix	1487-1507	21

Chain C: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1377-1380	4
α-helix	1381-1396	16
β-strand	1398	1	3
β-strand	1422	1	3
α-helix	1423-1426	4
α-helix	1430-1432	3
α-helix	1437-1442	6
α-helix	1449-1457	9
α-helix	1464-1481	18
α-helix	1483	1
α-helix	1487-1506	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable global transcription activator SNF2L2	A, B, C	protein	123	Homo sapiens	P51531 (AlphaFold model)

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

>9QAD_1 Probable global transcription activator SNF2L2 (chains A, B, C)
SMAEKLSPNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELPEYYELIRKPVD
FKKIKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSARQKIAK
EEE

Ligands and cofactors

ID	Name	Formula	Copies
A1I45	5-oxidanyl-2-(phenylmethyl)-1,9-dihydropyrimido[4,5-b]indol-4-one	C17 H13 N3 O2	3
ZN	Zinc ion	Zn	3

Primary citation

Discovery of Pyrimidoindolones as Novel Family VIII Bromodomain Binders. Boerth, J.A., Schimpl, M., Lucas, S.C.C. et al. ACS Med Chem Lett (2025) 16:1073-1079. DOI 10.1021/acsmedchemlett.5c00120 · 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
9D12 2.1 Å, Smarca2 Bromodomain in complex with compound 15

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