8AHC: BRD9 bromodomain with BI-7189

Crystal structure of the BRD9 bromodomain with BI-7189. Determined by X-ray diffraction at 1.5 Å resolution. Released 21 Jun 2023.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,187
Mol. weight: 29.16 kDa
Ligands: M2O
Released: 21 Jun 2023

Explore 8AHC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8AHC contains 14 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.

Chains A and B: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	24-38	15
α-helix	48-50	3
α-helix	57-60	4
α-helix	67-75	9
α-helix	82-99	18
α-helix	105-120	16
α-helix	123-132	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bromodomain-containing protein 9	A, B	protein	123	Homo sapiens	Q9H8M2 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8AHC_1 Bromodomain-containing protein 9 (chains A, B)
SMLKLSAENESTPIQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMK
DKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSKERLLALKR
SMS

Ligands and cofactors

ID	Name	Formula	Copies
M2O	[2,6-dimethoxy-4-(1,2,5-trimethyl-6-oxidanylidene-pyridin-3-yl)phenyl]methyl-di…	C19 H27 N2 O3	2

Primary citation

Discovery of a Chemical Probe to Study Implications of BPTF Bromodomain Inhibition in Cellular and in vivo Experiments. Martinelli, P., Schaaf, O., Mantoulidis, A. et al. ChemMedChem (2023) 18:e202200686-e202200686. DOI 10.1002/cmdc.202200686 · 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
9ZU3 1.15 Å, Crystal structure of BRD9 bromodomain bound to BZ1
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

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