6V1B: Bromodomain of human BRD9

Crystal structure of the bromodomain of human BRD9 bound to I-BRD9. Determined by X-ray diffraction at 1.35 Å resolution. Released 11 Mar 2020.

Method: X-ray diffraction
Resolution: 1.35 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,275
Mol. weight: 29.56 kDa
Ligands: H1B
Released: 11 Mar 2020

Explore 6V1B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6V1B 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	140-153	14
α-helix	164-166	3
α-helix	173-176	4
α-helix	183-191	9
α-helix	198-215	18
α-helix	221-236	16
α-helix	239-248	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

>6V1B_1 Bromodomain-containing protein 9 (chains A, B)
SMLKLSAENESTPIQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMK
DKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSKERLLALKR
SMS

Ligands and cofactors

ID	Name	Formula	Copies
H1B	N'-[1,1-bis(oxidanylidene)thian-4-yl]-5-ethyl-4-oxidanylidene-7-[3-(trifluorome…	C22 H22 F3 N3 O3 S2	2

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

Primary citation

Structural Basis of Inhibitor Selectivity in the BRD7/9 Subfamily of Bromodomains. Karim, R.M., Chan, A., Zhu, J.Y. et al. J Med Chem (2020) 63:3227-3237. DOI 10.1021/acs.jmedchem.9b01980 · 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-…
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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