8YME | pdb_00008yme

BRD4-BD1 in complex with N-cyclohexyl-1-methyl-6-{[5-methyl-7-(1-methylpyrazol-3-yl)-4-oxo-pyrazolo[4,3-c]pyridin-2-yl]methyl}azepan-1-ium-4-carboxamide 2,2,2-trifluoroacetate

• PDB DOI: https://doi.org/10.2210/pdb8YME/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-09 Released: 2025-03-12 
• Deposition Author(s): Sasaki, C., Miyaguchi, I., Hagihara, S., Ishizawa, K., Endo, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free: 
  0.186 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.166 (DCC) 

Starting Model: experimental

Literature

Discovery of a potent, orally available pyrazolopyridone derivative as a novel selective BET BD1 Inhibitor (Part 2).

Hagihara, S., Ishizawa, K., Soga, K., Honjo, T., Takai, S., Kawano, Y., Kikuchi, M., Nishidate, A., Matsumoto, F., Murase, M., Hashimoto, N., Sasaki, C., Miyaguchi, I., Okada, O., Akashi, T., Nakayama, S., Ogasawara, Y., Endo, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.86 kDa 
• Atom Count: 1,248 
• Modelled Residue Count: 127 
• Deposited Residue Count: 128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	128	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1LZZ (Subject of Investigation/LOI)	B [auth A]	(4R,6S)-N-cyclohexyl-1-methyl-6-[[5-methyl-7-(1-methylpyrazol-3-yl)-4-oxidanylidene-pyrazolo[4,3-c]pyridin-2-yl]methyl]azepane-4-carboxamide C26 H37 N7 O2 DFZFJCROMQNFGV-OALUTQOASA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free:  0.186 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.166 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.05	α = 90
b = 49.35	β = 90
c = 61.06	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Sasaki, C., Miyaguchi, I., Hagihara, S., Ishizawa, K., Endo, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release