7MRH

Crystal structure of the first bromodomain (BD1) of human BRDT bound to NC-II-259


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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Ligand Structure Quality Assessment 


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Literature

Bivalent BET Bromodomain Inhibitors Confer Increased Potency and Selectivity for BRDT via Protein Conformational Plasticity.

Guan, X.Cheryala, N.Karim, R.M.Chan, A.Berndt, N.Qi, J.Georg, G.I.Schonbrunn, E.

(2022) J Med Chem 

  • DOI: 10.1021/acs.jmedchem.2c00453
  • Primary Citation of Related Structures:  
    7L9M, 7LA9, 7MR5, 7MR6, 7MR7, 7MR9, 7MRA, 7MRB, 7MRC, 7MRD, 7MRG, 7MRH, 8CZA

  • PubMed Abstract: 
  • Bromodomain and extraterminal domain (BET) proteins are important regulators of gene transcription and chromatin remodeling. BET family members BRD4 and BRDT are validated targets for cancer and male contraceptive drug development, respectively. Due to the high structural similarity of the acetyl-lysine binding sites, most reported inhibitors lack intra-BET selectivity ...

    Bromodomain and extraterminal domain (BET) proteins are important regulators of gene transcription and chromatin remodeling. BET family members BRD4 and BRDT are validated targets for cancer and male contraceptive drug development, respectively. Due to the high structural similarity of the acetyl-lysine binding sites, most reported inhibitors lack intra-BET selectivity. We surmised that protein-protein interactions induced by bivalent inhibitors may differ between BRD4 and BRDT, conferring an altered selectivity profile. Starting from nonselective monovalent inhibitors, we developed cell-active bivalent BET inhibitors with increased activity and selectivity for BRDT. X-ray crystallographic and solution studies revealed unique structural states of BRDT and BRD4 upon interaction with bivalent inhibitors. Varying spacer lengths and symmetric vs unsymmetric connections resulted in the same dimeric states, whereas different chemotypes induced different dimers. The findings indicate that the increased intra-BET selectivity of bivalent inhibitors is due to the differential plasticity of BET bromodomains upon inhibitor-induced dimerization.


    Organizational Affiliation

    Moffitt Cancer Center, Drug Discovery Department, 12902 Magnolia Drive, Tampa, Florida 33612, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain testis-specific proteinA, B113Homo sapiensMutation(s): 0 
Gene Names: BRDT
UniProt & NIH Common Fund Data Resources
Find proteins for Q58F21 (Homo sapiens)
Explore Q58F21 
Go to UniProtKB:  Q58F21
PHAROS:  Q58F21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58F21
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZMJ (Subject of Investigation/LOI)
Query on ZMJ

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N-[3-(2-methyl-1-oxo-1,2-dihydroisoquinolin-4-yl)phenyl]ethanesulfonamide
C18 H18 N2 O3 S
QIEVBHRUPLMWFP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.64α = 90
b = 29.82β = 98.56
c = 73.22γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United States1U54HD093540

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release