8YMI: BRD4-BD1

BRD4-BD1 in complex with 2-{[(3S)-1-benzylpyrrolidin-3-yl]methyl}-5-methyl-7-(1-methylpyrazol-3-yl)pyrazolo[4,3-c]pyridin-4-one. Determined by X-ray diffraction at 1.01 Å resolution. Released 12 Mar 2025.

Method: X-ray diffraction
Resolution: 1.01 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,265
Mol. weight: 15.81 kDa
Ligands: A1LZF
Released: 12 Mar 2025

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

Secondary structure: helices and β-sheets

8YMI contains 11 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: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	45-49	5
α-helix	61-65	5
α-helix	66-71	6
α-helix	72-75	4
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
α-helix	164-166	3

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

>8YMI_1 Bromodomain-containing protein 4 (chains A)
GSMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKI
IKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQK
INELPTEE

Ligands and cofactors

ID	Name	Formula	Copies
A1LZF	2-{[(3S)-1-benzylpyrrolidin-3-yl]methyl}-5-methyl-7-(1-methylpyrazol-3-yl)pyraz…	C23 H26 N6 O	1

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

Primary citation

Discovery of a potent, orally available pyrazolopyridone derivative as a novel selective BET BD1 Inhibitor (Part 2). Hagihara, S., Ishizawa, K., Soga, K. et al. To be published.

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…
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
7ZA8 1.04 Å, BRD4 in complex with FragLite6

Browse structure collections

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