6K05

Crystal structure of BRD2(BD1)with ligand BY27 bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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Ligand Structure Quality Assessment 


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Literature

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: 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) ...

    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. Electronic address: yjzhao@simm.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 2A, B, C122Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25440
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CQF (Subject of Investigation/LOI)
Query on CQF

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]
(6~{R})-~{N}-(4-chlorophenyl)-1-methyl-8-(1-methylpyrazol-4-yl)-5,6-dihydro-4~{H}-[1,2,4]triazolo[4,3-a][1]benzazepin-6-amine
C22 H21 Cl N6
MDRXOFSNECSECW-HXUWFJFHSA-N
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
F [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CQF Binding MOAD:  6K05 Ki: 95.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing

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