5IGK

Crystal structure of the first bromodomain of human BRD4 in complex with bromosporine (BSP)

• PDB DOI:  https://doi.org/10.2210/pdb5IGK/pdb

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


• Deposited: 2016-02-28 Released: 2016-10-19 
• Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., von Delft, F., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.200 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 

Literature

Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia.

Picaud, S., Leonards, K., Lambert, J.P., Dovey, O., Wells, C., Fedorov, O., Monteiro, O., Fujisawa, T., Wang, C.Y., Lingard, H., Tallant, C., Nikbin, N., Guetzoyan, L., Ingham, R., Ley, S.V., Brennan, P., Muller, S., Samsonova, A., Gingras, A.C., Schwaller, J., Vassiliou, G., Knapp, S., Filippakopoulos, P.

(2016) Sci Adv 2: e1600760-e1600760

• PubMed: 27757418 
• DOI: https://doi.org/10.1126/sciadv.1600760
• Primary Citation of Related Structures:  
  5IGK, 5IGL, 5IGM


• PubMed Abstract: 
  

Bromodomains (BRDs) have emerged as compelling targets for cancer therapy. The development of selective and potent BET (bromo and extra-terminal) inhibitors and their significant activity in diverse tumor models have rapidly translated into clinical studies and have motivated drug development efforts targeting non-BET BRDs. However, the complex multidomain/subunit architecture of BRD protein complexes complicates predictions of the consequences of their pharmacological targeting. To address this issue, we developed a promiscuous BRD inhibitor [bromosporine (BSP)] that broadly targets BRDs (including BETs) with nanomolar affinity, creating a tool for the identification of cellular processes and diseases where BRDs have a regulatory function. As a proof of principle, we studied the effects of BSP on leukemic cell lines known to be sensitive to BET inhibition and found, as expected, strong antiproliferative activity. Comparison of the modulation of transcriptional profiles by BSP after a short exposure to the inhibitor resulted in a BET inhibitor signature but no significant additional changes in transcription that could account for inhibition of other BRDs. Thus, nonselective targeting of BRDs identified BETs, but not other BRDs, as master regulators of context-dependent primary transcription response.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.; Ludwig Institute for Cancer Research, University of Oxford, Oxford OX3 7DQ, U.K.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.57 kDa 
• Atom Count: 1,206 
• 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	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMF	C [auth A]	Bromosporine C17 H20 N6 O4 S UYBRROMMFMPJAN-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BMF	Binding MOAD:  5IGK	Kd: 41.8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.200 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.465	α = 90
b = 43.848	β = 90
c = 78.016	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-19 
Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., von Delft, F., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2016-10-19
  Type: Initial release
  
• Version 1.1: 2016-11-02
  Changes: Database references