Crystal structure of BRD2(BD1)with ligand BY27 bound

Experimental Data Snapshot

  • Resolution: 1.94 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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Discovery, structural insight, and bioactivities of BY27 as a selective inhibitor of the second bromodomains of BET proteins.

Chen, D.Lu, T.Yan, Z.Lu, W.Zhou, F.Lyu, X.Xu, B.Jiang, H.Chen, K.Luo, C.Zhao, Y.

(2019) Eur J Med Chem 182: 111633-111633

  • DOI: https://doi.org/10.1016/j.ejmech.2019.111633
  • Primary Citation of Related Structures:  
    6K04, 6K05

  • PubMed Abstract: 

    Recently, selective inhibition of BET BD2 is emerging as a promising strategy for drug discovery. Despite significant progress in this area, systematic studies of selective BET BD2 inhibitors are still few. In this study, we report the discovery of a potent and selective BET BD2 inhibitor BY27 (47). Our high resolution co-crystal structures of 47/BRD2 BD1 and BD2 showed that the triazole group of 47, water molecules, H433 and N429 in BRD2 BD2 established a water-bridged H-bonding network, which is responsible for the observed selectivities. DNA microarray analysis of HepG2 cells treated with 47 or OTX015 demonstrated the transcriptome impact differences between a BET BD2 selective inhibitor and a pan BET inhibitor. In a MV4-11 mouse xenograft model, 47 caused 67% of tumor growth inhibition and was less toxic than a pan BET inhibitor 1 at high doses. We conclude that the improved safety profile of selective BET BD2 inhibitors warrant future studies in BET associated diseases.

  • Organizational Affiliation

    State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd., Shanghai, 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 2
A, B, C
122Homo 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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CQF (Subject of Investigation/LOI)
Query on CQF

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]
C22 H21 Cl N6
Query on MES

Download Ideal Coordinates CCD File 
C6 H13 N O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
CQF Binding MOAD:  6K05 Ki: 95.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.94 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.133α = 90
b = 55.735β = 94.33
c = 67.434γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (China)China81625022
National Science Foundation (China)China91853205
National Science Foundation (China)China81821005

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Derived calculations
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description