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: 18.31 kDa 
• Atom Count: 1377 
• Residue Count: 127 
• Unique protein chains: 1

4UYD

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 1,3-dimethyl-2-oxo-2,3- dihydro-1H-1,3-benzodiazole-5-carboxamide

• DOI: 10.2210/pdb4UYD/pdb

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


• Deposited: 2014-08-30 Released: 2014-09-17 
• Deposition Author(s): Chung, C., Bamborough, P., Demont, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.188 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

Literature

1,3-Dimethyl Benzimidazolones are Potent, Selective Inhibitors of the Brpf1 Bromodomain.

Demont, E.H., Bamborough, P., Chung, C.W., Craggs, P.D., Fallon, D., Gordon, L.J., Grandi, P., Hobbs, C.I., Hussain, J., Jones, E.J., Le Gall, A., Michon, A.M., Mitchell, D.J., Prinjha, R.K., Roberts, A.D., Sheppard, R.J., Watson, R.J.

(2014) ACS Med Chem Lett 5: 1190

• PubMed: 25408830 
• DOI: 10.1021/ml5002932
• Primary Citation of Related Structures:  
  4UYD, 4UYE


• PubMed Abstract: 
  

The BRPF (bromodomain and PHD finger-containing) protein family are important scaffolding proteins for assembly of MYST histone acetyltransferase complexes. Here, we report the discovery, binding mode, and structure-activity relationship (SAR) of the first potent, selective series of inhibitors of the BRPF1 bromodomain.

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Organizational Affiliation: 

Epinova Discovery Performance Unit and Molecular Discovery Research, GlaxoSmithKline , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BROMODOMAIN-CONTAINING PROTEIN 4	A	153	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
NIH Common Fund Data Resources
PHAROS  O60885 GTEx  ENSG00000141867

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V1T	A	1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazole-5-carboxamide C10 H11 N3 O2 BRBLVCVSNVSPMT-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 %)
V1T	IC50:  79433   nM  BindingDB
V1T	IC50:  79400   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.188 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.42	α = 90
b = 44.2	β = 90
c = 78.26	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-08-30 
• Released Date: 2014-09-17 
Deposition Author(s): Chung, C., Bamborough, P., Demont, E.

Revision History 

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2014-12-03
  Changes: Database references