7P6W

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH compound 3bg

• PDB DOI: https://doi.org/10.2210/pdb7P6W/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-07-18 Released: 2021-10-06 
• Deposition Author(s): Chung, C.

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Experimental Data Snapshot

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

Starting Model: other

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

• PubMed: 34328642 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 15.76 kDa 
• Atom Count: 1,367 
• Modelled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A [auth AAA]	127	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5YY (Subject of Investigation/LOI)	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 = 42.351	α = 90
b = 52.103	β = 90
c = 57.176	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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