7L9J

Crystal structure of the second bromodomain (BD2) of human BRD2 bound to Ro3280


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors.

Karim, R.M.Bikowitz, M.J.Chan, A.Zhu, J.Y.Grassie, D.Becker, A.Berndt, N.Gunawan, S.Lawrence, N.J.Schonbrunn, E.

(2021) J Med Chem 64: 15772-15786

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01096
  • Primary Citation of Related Structures:  
    5V67, 5VBO, 5VBP, 5VBQ, 5VBR, 7BJY, 7K6G, 7K6H, 7KO0, 7L6D, 7L72, 7L73, 7L9G, 7L9J, 7L9K, 7L9L, 7LAH, 7LAI, 7LAJ, 7LAK, 7LAU, 7LAY, 7LAZ, 7LB4, 7LBT, 7LEJ, 7LEK, 7LEL, 7LEM

  • PubMed Abstract: 

    BRD4 and other members of the bromodomain and extraterminal (BET) family of proteins are promising epigenetic targets for the development of novel therapeutics. Among the reported BRD4 inhibitors are dihydropteridinones and benzopyrimidodiazepinones originally designed to target the kinases PLK1, ERK5, and LRRK2. While these kinase inhibitors were identified as BRD4 inhibitors, little is known about their binding potential and structural details of interaction with the other BET bromodomains. We comprehensively characterized a series of known and newly identified dual BRD4-kinase inhibitors against all eight individual BET bromodomains. A detailed analysis of 23 novel cocrystal structures of BET-kinase inhibitor complexes in combination with direct binding assays and cell signaling studies revealed significant differences in molecular shape complementarity and inhibitory potential. Collectively, the data offer new insights into the action of kinase inhibitors across BET bromodomains, which may aid the development of drugs to inhibit certain BET proteins and kinases differentially.


  • Organizational Affiliation

    Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 2114Homo 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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
79C (Subject of Investigation/LOI)
Query on 79C

Download Ideal Coordinates CCD File 
B [auth A]4-[(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino]-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide
C27 H35 F2 N7 O3
DJNZZLZKAXGMMC-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.33α = 90
b = 72.148β = 90
c = 31.938γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Database references
  • Version 1.2: 2021-11-24
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description