7P6W

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH compound 3bg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 

Starting Model: other
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

One-Step Synthesis of Photoaffinity Probes for Live-Cell MS-Based Proteomics.

Fallon, D.J.Lehmann, S.Chung, C.W.Phillipou, A.Eberl, C.Fantom, K.G.M.Zappacosta, F.Patel, V.K.Bantscheff, M.Schofield, C.J.Tomkinson, N.C.O.Bush, J.T.

(2021) Chemistry 27: 17880-17888

  • DOI: https://doi.org/10.1002/chem.202102036
  • Primary Citation of Related Structures:  
    7P6V, 7P6W, 7P6Y

  • PubMed Abstract: 

    We present a one-step Ugi reaction protocol for the expedient synthesis of photoaffinity probes for live-cell MS-based proteomics. The reaction couples an amine affinity function with commonly used photoreactive groups, and a variety of handle functionalities. Using this technology, a series of pan-BET (BET: bromodomain and extra-terminal domain) selective bromodomain photoaffinity probes were obtained by parallel synthesis. Studies on the effects of photoreactive group, linker length and irradiation wavelength on photocrosslinking efficiency provide valuable insights into photoaffinity probe design. Optimal probes were progressed to MS-based proteomics to capture the BET family of proteins from live cells and reveal their potential on- and off-target profiles.


  • Organizational Affiliation

    GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A [auth AAA]127Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
GTEx:  ENSG00000141867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5YY (Subject of Investigation/LOI)
Query on 5YY

Download Ideal Coordinates CCD File 
B [auth AAA]ethyl 2-(2-(4-azido-N-((2-(1,5-dimethyl-6-oxo-1,6-dihydropyridin-3-yl)-1-((tetrahydro-2H-pyran-4-yl)methyl)-1H-benzo[d]imidazol-6-yl)methyl)benzamido)acetamido)acetate
C34 H39 N8 O6
GHCAGGKSFJHAIR-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.351α = 90
b = 52.103β = 90
c = 57.176γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-10-06 
  • Deposition Author(s): Chung, C.

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2021-12-29
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Derived calculations, Refinement description