6SWP | pdb_00006swp

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH iBET-BD2 (GSK046)

• PDB DOI: https://doi.org/10.2210/pdb6SWP/pdb

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


• Deposited: 2019-09-22 Released: 2020-04-01 
• Deposition Author(s): Chung, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.193 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.154 (Depositor) 

Literature

Selective targeting of BD1 and BD2 of the BET proteins in cancer and immunoinflammation.

Gilan, O., Rioja, I., Knezevic, K., Bell, M.J., Yeung, M.M., Harker, N.R., Lam, E.Y.N., Chung, C.W., Bamborough, P., Petretich, M., Urh, M., Atkinson, S.J., Bassil, A.K., Roberts, E.J., Vassiliadis, D., Burr, M.L., Preston, A.G.S., Wellaway, C., Werner, T., Gray, J.R., Michon, A.M., Gobbetti, T., Kumar, V., Soden, P.E., Haynes, A., Vappiani, J., Tough, D.F., Taylor, S., Dawson, S.J., Bantscheff, M., Lindon, M., Drewes, G., Demont, E.H., Daniels, D.L., Grandi, P., Prinjha, R.K., Dawson, M.A.

(2020) Science 368: 387-394

• PubMed: 32193360 
• DOI: https://doi.org/10.1126/science.aaz8455
• Primary Citation Related Structures: 
  6SWN, 6SWO, 6SWP, 6SWQ


• PubMed Abstract: 
  

  The two tandem bromodomains of the BET (bromodomain and extraterminal domain) proteins enable chromatin binding to facilitate transcription. Drugs that inhibit both bromodomains equally have shown efficacy in certain malignant and inflammatory conditions. To explore the individual functional contributions of the first (BD1) and second (BD2) bromodomains in biology and therapy, we developed selective BD1 and BD2 inhibitors. We found that steady-state gene expression primarily requires BD1, whereas the rapid increase of gene expression induced by inflammatory stimuli requires both BD1 and BD2 of all BET proteins. BD1 inhibitors phenocopied the effects of pan-BET inhibitors in cancer models, whereas BD2 inhibitors were predominantly effective in models of inflammatory and autoimmune disease. These insights into the differential requirement of BD1 and BD2 for the maintenance and induction of gene expression may guide future BET-targeted therapies.

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Organizational Affiliation: 
• Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK.
Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, Heidelberg, Germany.
Promega Corporation, Madison, WI, USA.
Computational Biology, GlaxoSmithKline, Collegeville, PA, USA.
Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia.
Epigenetics RU, GlaxoSmithKline Medicines Research Centre, Stevenage, UK. [e-mail] [e-mail].
Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. [e-mail] [e-mail].

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: 13.97 kDa 
• Atom Count: 1,265 
• Modeled Residue Count: 112 
• Deposited Residue Count: 115 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A [auth AAA]	115	Homo sapiens	Mutation(s): 0  Gene Names: BRD2, KIAA9001, RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens) Explore P25440  Go to UniProtKB:  P25440
PHAROS:  P25440 GTEx:  ENSG00000204256

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LW5 (Subject of Investigation/LOI)	D [auth AAA]	4-acetamido-3-fluoranyl-~{N}-(4-oxidanylcyclohexyl)-5-[(1~{S})-1-phenylethoxy]benzamide C23 H27 F N2 O4 FRBRZGLUFOZRGD-JVPBZIDWSA-N
EDO	B [auth AAA], C [auth AAA]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LW5	BindingDB:  6SWP	IC50: min: 251, max: 1.00e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.193 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.154 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.201	α = 90
b = 52.39	β = 90
c = 32.024	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-01 
Deposition Author(s): Chung, C.

Revision History  

• Version 1.0: 2020-04-01
  Type: Initial release
  
• Version 1.1: 2020-05-06
  Changes: Database references
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references, Derived calculations