4UYD

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


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 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/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.


  • Organizational Affiliation

    Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline , Meyerhofstrasse 1, 69117 Heidelberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BROMODOMAIN-CONTAINING PROTEIN 4153Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
GTEx:  ENSG00000141867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V1T
Query on V1T

Download Ideal Coordinates CCD File 
D [auth A]1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazole-5-carboxamide
C10 H11 N3 O2
BRBLVCVSNVSPMT-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
B [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
V1T Binding MOAD:  4UYD IC50: 7.94e+4 (nM) from 1 assay(s)
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 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.42α = 90
b = 44.2β = 90
c = 78.26γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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