8Z69

Crystal Structure of the second bromodomain of human BRD2 BD2 in complex with the inhibitor Y13195


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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
BRD2_HUMAN
A, B, C, D
136Homo sapiensMutation(s): 0 
Gene Names: BRD2KIAA9001RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens)
Explore P25440 
Go to UniProtKB:  P25440
PHAROS:  P25440
GTEx:  ENSG00000204256 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25440
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L0Y (Subject of Investigation/LOI)
Query on A1L0Y

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
O [auth C],
V [auth D]
7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methyl-2-(2-phenyl-1H-imidazol-5-yl)furo[3,2-c]pyridin-4(5H)-one
C34 H30 F N3 O4
VUSLJIDUEUBGQH-UHFFFAOYSA-N
PEG
Query on PEG

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AA [auth D]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth B],
P [auth C],
Q [auth C],
R [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
DA [auth D]
K [auth B]
L [auth B]
BA [auth D],
CA [auth D],
DA [auth D],
K [auth B],
L [auth B],
N [auth C],
S [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT
Query on FMT

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EA [auth D]
F [auth A]
G [auth A]
H [auth A]
M [auth C]
EA [auth D],
F [auth A],
G [auth A],
H [auth A],
M [auth C],
T [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
FA [auth D],
U [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.27α = 90
b = 95.53β = 90
c = 110.71γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
xia2data 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