5I40: BRD9

BRD9 in complex with Cpd1 (6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one). Determined by X-ray diffraction at 1.04 Å resolution. Released 12 Oct 2016.

Method: X-ray diffraction
Resolution: 1.04 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,095
Mol. weight: 12.36 kDa
Ligands: 67N
Released: 12 Oct 2016

Explore 5I40 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5I40 contains 6 α-helices and 0 β-strands across 1 chain. 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: 6 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	105-122	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bromodomain-containing protein 9	A	protein	102	Homo sapiens	Q9H8M2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5I40_1 Bromodomain-containing protein 9 (chains A)
STPIQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKS
VTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSK

Ligands and cofactors

ID	Name	Formula	Copies
67N	6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one	C8 H8 N2 O	1

Water and common crystallization additives (PEG, EDO) are not listed.

Primary citation

Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains. Crawford, T.D., Tsui, V., Flynn, E.M. et al. J Med Chem (2016) 59:5391-5402. DOI 10.1021/acs.jmedchem.6b00264 · 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]…
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
4YYI 1.5 Å, Crystal structure of BRD9 Bromodomain bound to an acetylated peptide

Browse structure collections

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