Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 14.07 kDa 
• Atom Count: 1095 
• Modelled Residue Count: 110 
• Deposited Residue Count: 114 
• Unique protein chains: 1

4MR5

Crystal Structure of the second bromodomain of human BRD2 in complex with a quinazolinone ligand (RVX-OH)

• DOI: 10.2210/pdb4MR5/pdb

• Classification: TRANSCRIPTION/TRANSCRIPTION inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-09-17 Released: 2013-11-27 
• Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., Martin, S., Fedorov, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.170 
• R-Value Work: 0.136 
• R-Value Observed: 0.137 

Literature

RVX-208, an inhibitor of BET transcriptional regulators with selectivity for the second bromodomain.

Picaud, S., Wells, C., Felletar, I., Brotherton, D., Martin, S., Savitsky, P., Diez-Dacal, B., Philpott, M., Bountra, C., Lingard, H., Fedorov, O., Muller, S., Brennan, P.E., Knapp, S., Filippakopoulos, P.

(2013) Proc Natl Acad Sci U S A 110: 19754-19759

• PubMed: 24248379 
• DOI: 10.1073/pnas.1310658110
• Primary Citation of Related Structures:  
  4MR3, 4MR4, 4MR5, 4MR6


• PubMed Abstract: 
  

Bromodomains have emerged as attractive candidates for the development of inhibitors targeting gene transcription. Inhibitors of the bromo and extraterminal (BET) family recently showed promising activity in diverse disease models. However, the pleiotropic nature of BET proteins regulating tissue-specific transcription has raised safety concerns and suggested that attempts should be made for domain-specific targeting. Here, we report that RVX-208, a compound currently in phase II clinical trials, is a BET bromodomain inhibitor specific for second bromodomains (BD2s). Cocrystal structures revealed binding modes of RVX-208 and its synthetic precursor, and fluorescent recovery after photobleaching demonstrated that RVX-208 displaces BET proteins from chromatin. However, gene-expression data showed that BD2 inhibition only modestly affects BET-dependent gene transcription. Our data demonstrate the feasibility of specific targeting within the BET family resulting in different transcriptional outcomes and highlight the importance of BD1 in transcriptional regulation.

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Organizational Affiliation: 

Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A	114	Homo sapiens	Mutation(s): 0  Gene Names: BRD2, KIAA9001, RING3
Find proteins for P25440 (Homo sapiens) Explore P25440  Go to UniProtKB:  P25440
NIH Common Fund Data Resources
PHAROS:  P25440 GTEx:  ENSG00000204256

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1K0	A	2-[4-(2-hydroxyethoxy)-3,5-dimethylphenyl]-5,7-dimethoxyquinazolin-4(3H)-one C20 H22 N2 O5 NETXMUIMUZJUTB-UHFFFAOYSA-N
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
1K0	Kd :  251   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.170 
• R-Value Work: 0.136 
• R-Value Observed: 0.137 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.22	α = 90
b = 72.008	β = 90
c = 32.039	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-09-17 
• Released Date: 2013-11-27 
Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., Martin, S., Fedorov, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2013-11-27
  Type: Initial release
  
• Version 1.1: 2014-01-22
  Changes: Database references