8YMH: BRD4-BD1

BRD4-BD1 in complex with 5-methyl-2-{[(2R)-2-methyl-4-methylsulfonyl-piperazin-1-yl]methyl}-7-(1-methylpyrazol-3-yl)furo[3,2-c]pyridin-4-one. Determined by X-ray diffraction at 1.04 Å resolution. Released 12 Mar 2025.

Method: X-ray diffraction
Resolution: 1.04 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,233
Mol. weight: 15.7 kDa
Ligands: A1LZE
Released: 12 Mar 2025

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

Secondary structure: helices and β-sheets

8YMH contains 10 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: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	44-49	6
α-helix	61-65	5
α-helix	66-71	6
α-helix	72-74	3
α-helix	81-83	3
α-helix	89-92	4
α-helix	97-100	4
α-helix	107-115	9
α-helix	122-139	18
α-helix	145-162	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bromodomain-containing protein 4	A	protein	128	Homo sapiens	O60885 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8YMH_1 Bromodomain-containing protein 4 (chains A)
GSMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKI
IKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQK
INELPTEE

Ligands and cofactors

ID	Name	Formula	Copies
A1LZE	5-methyl-2-{[(2R)-2-methyl-4-methylsulfonyl-piperazin-1-yl]methyl}-7-(1-methylp…	C19 H25 N5 O4 S	1

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

Primary citation

Discovery of a potent, orally available furopyridine derivative as a novel selective bromodomain and extra-terminal domain (BET)-first bromodomain (BD1) inhibitor. Hagihara, S., Ishizawa, K., Kikuchi, M. et al. Bioorg Med Chem Lett (2024) 109:129848-129848. DOI 10.1016/j.bmcl.2024.129848 · PubMed

Other PDB entries of the same protein (UniProt O60885 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4QB3 0.94 Å, Crystal structure of the first bromodomain of human BRD4 in complex with Olinone
6FO5 0.95 Å, First domain of human bromodomain BRD4 in complex with inhibitor #17
7Z9W 0.99 Å, BRD4 in complex with FragLite1
4ZC9 0.99 Å, Crystal Structure of the BRD4a/DB-2-190 complex
9P34 0.99 Å, Crystal structure of the Bromo domain 1 in human Bromodomain Containing Protein 4 with a…
6I7Y 1.0 Å, Crystal Structure of the first bromodomain of BRD4 in complex with RT56
7ZAJ 1.0 Å, BRD4 in complex with FragLite16
8YMG 1.01 Å, BRD4-BD1 in complex with 7-[4-chloro-1-(tetrahydropyran-4-ylmethyl)imidazol-2-yl]-5-methy…
8YMI 1.01 Å, BRD4-BD1 in complex with 2-{[(3S)-1-benzylpyrrolidin-3-yl]methyl}-5-methyl-7-(1-methylpyr…
9P33 1.01 Å, Crystal structure of the Bromo domain 1 in human Bromodomain Containing Protein 4 with a…
8YMF 1.01 Å, BRD4-BD1 in complex with 7-[2-(cyclopropylmethoxy)phenyl]-5-methyl-2-[(1-methylsulfonyl-4…
7Z9Y 1.04 Å, BRD4 in complex with FragLite2

Browse structure collections

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