BROMODOMAIN OF HUMAN BRPF1 WITH N-1,3-dimethyl-2-oxo-6-(piperidin-1- yl)-2,3-dihydro-1H-1,3-benzodiazol-5-yl-2-methoxybenzamide

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

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This is version 1.2 of the entry. See complete history


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

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
118Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P55201 (Homo sapiens)
Explore P55201 
Go to UniProtKB:  P55201
PHAROS:  P55201
GTEx:  ENSG00000156983 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55201
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 9F9

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]
C22 H26 N4 O3
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
9F9 Binding MOAD:  4UYE Kd: 9.54 (nM) from 1 assay(s)
BindingDB:  4UYE IC50: min: 79, max: 1000 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.06α = 90
b = 68.12β = 126.1
c = 58.75γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

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