4UYD | pdb_00004uyd

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

• PDB DOI: https://doi.org/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 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.174 (Depositor) 
• R-Value Observed: 
  0.175 (Depositor) 

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: https://doi.org/10.1021/ml5002932
• Primary Citation 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.
Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline , Meyerhofstrasse 1, 69117 Heidelberg, Germany.
DMPK, GlaxoSmithKline , Park Road, Ware SG12 0DP, U.K.

Biological Assembly 1  

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: 1,377 
• Modeled Residue Count: 127 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BROMODOMAIN-CONTAINING PROTEIN 4	A	153	Homo sapiens	Mutation(s): 0
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V1T	D [auth A]	1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazole-5-carboxamide C10 H11 N3 O2 BRBLVCVSNVSPMT-UHFFFAOYSA-N
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
V1T	BindingDB:  4UYD	IC50: 7.94e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free:  0.188 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.174 (Depositor) 
• R-Value Observed: 0.175 (Depositor) 

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

• 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
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other