8ZMQ

Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.257 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of the First BRD4 Second Bromodomain (BD2)-Selective Inhibitors.

Li, J.Hu, Q.Zhu, R.Dong, R.Shen, H.Hu, J.Zhang, C.Zhang, X.Xu, T.Xiang, Q.Zhang, Y.Lin, B.Zhao, L.Wu, X.Xu, Y.

(2024) J Med Chem 67: 21577-21616

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02516
  • Primary Citation of Related Structures:  
    8Z69, 8ZM8, 8ZMB, 8ZMQ

  • PubMed Abstract: 

    Pan-BD2 inhibitors have been shown to retain an antileukemia effect and display less dose-limiting toxicities than pan-BET inhibitors. However, it is necessary to consider the potential off-target toxicity associated with the inhibition of four BET BD2 proteins. To date, no BRD4 BD2 domain selective inhibitor has been reported. Based on our previous pan-BD2 inhibitor 12 (XY153), we successfully identified 16o (XY221) as the first BRD4 BD2-selective inhibitor. 16o demonstrated potent binding affinity for BRD4 BD2 (IC 50 = 5.8 nM), along with high pan-BD2 selectivity (667-fold over BRD4 BD1) and BRD4 BD2 domain selectivity (9-32-fold over BRD2/3/T BD2). The BRD4 BD2 selectivity of 16o was further confirmed by the BLI assay, showing 66-144-fold selectivity over other BET BD2 domains. 16o exhibited good liver microsomal stability ( T 1/2 > 120 min) and pharmacokinetic properties ( F = 13.1%). These data indicate that 16o may serve as a valuable candidate for BRD4 BD2 advancing epigenetic research.


  • Organizational Affiliation

    China-New Zealand Joint Laboratory of Biomedicine and Health, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Biocomputing, Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BRD4_HUMAN
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
147Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
GTEx:  ENSG00000141867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L12 (Subject of Investigation/LOI)
Query on A1L12

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth E]
CA [auth F]
DA [auth G]
EA [auth H]
AA [auth D],
BA [auth E],
CA [auth F],
DA [auth G],
EA [auth H],
FA [auth I],
GA [auth J],
HA [auth K],
IA [auth L],
KA [auth M],
MA [auth N],
OA [auth O],
PA [auth P],
QA [auth Q],
RA [auth R],
SA [auth S],
TA [auth T],
U [auth A],
X [auth B],
Z [auth C]
2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one
C40 H44 F N3 O4
HZYKAGKNCZZUQL-PLKAPHTHSA-N
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
JA [auth L]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS (Subject of Investigation/LOI)
Query on DMS

Download Ideal Coordinates CCD File 
LA [auth M],
NA [auth N],
V [auth A],
W [auth B],
Y [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.257 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.913α = 90
b = 125.108β = 90.04
c = 300.352γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81673357

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release
  • Version 1.1: 2024-12-25
    Changes: Database references