9ZU3: BRD9 bromodomain

Crystal structure of BRD9 bromodomain bound to BZ1. Determined by X-ray diffraction at 1.15 Å resolution. Released 16 Sept 2026.

Method: X-ray diffraction
Resolution: 1.15 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,300
Mol. weight: 30.82 kDa
Ligands: A1C4C
Released: 16 Sept 2026

Explore 9ZU3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9ZU3 contains 10 α-helices and 0 β-strands across 2 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: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	140-153	14
α-helix	173-176	4
α-helix	183-191	9
α-helix	198-215	18
α-helix	221-237	17

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	140-154	15
α-helix	173-176	4
α-helix	183-191	9
α-helix	198-215	18
α-helix	221-238	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bromodomain-containing protein 9	A, B	protein	129	Homo sapiens	Q9H8M2 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9ZU3_1 Bromodomain-containing protein 9 (chains A, B)
MGSSHHHHHHHHHSSGENLYFQGAENESTPIQQLLEHFLRQLQRKDPHGFFAFPVTDAIA
PGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKIL
HAGFKMMSK

Ligands and cofactors

ID	Name	Formula	Copies
A1C4C	5-[4-(2-aminoethyl)anilino]-4-chloro-2-methylpyridazin-3(2H)-one	C13 H15 Cl N4 O	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Differential Water Networks Guide Selectivity Optimization of a Cell Active BPTF Inhibitor in Neuroblastoma. Babu, K., Tsou, C.J., Das, S. et al. Angew Chem Int Ed Engl (2026):e4580510-e4580510. DOI 10.1002/anie.4580510 · PubMed

Other PDB entries of the same protein (UniProt Q9H8M2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BQA 1.03 Å, BRD9 bromodomain in complex with 3-(6-(but-3-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]…
5I40 1.04 Å, BRD9 in complex with Cpd1 (6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one)
9ZU4 1.05 Å, Crystal structure of BRD9 bromodomain bound to BZ2
5I7X 1.18 Å, BRD9 in complex with Cpd2 (N,N-dimethyl-3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]py…
6Y7K 1.2 Å, Structure of the BRD9 bromodomain and compound 27
4UIT 1.3 Å, BROMODOMAIN OF HUMAN BRD9 WITH 7-(3,4-dimethoxyphenyl)-2-(4-…
6V1B 1.35 Å, Crystal structure of the bromodomain of human BRD9 bound to I-BRD9
5JI8 1.42 Å, Crystal structure of the BRD9 bromodomain and hit 1
4YY6 1.45 Å, Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide
5I7Y 1.45 Å, BRD9 in complex with Cpd4 ((E)-3-(6-(but-2-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]py…
4YY4 1.47 Å, Crystal structure of BRD9 Bromodomain bound to DMSO
4YYI 1.5 Å, Crystal structure of BRD9 Bromodomain bound to an acetylated peptide

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