5G4S

BROMODOMAIN OF HUMAN BRPF1 WITH N-1,3-dimethyl-6-2R-2- methylpiperazin-1-yl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl-N- ethyl-2-methoxybenzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Gsk6853, a Chemical Probe for Inhibition of the Brpf1 Bromodomain.

Bamborough, P.Barnett, H.A.Becher, I.Bird, M.J.Chung, C.Craggs, P.D.Demont, E.H.Diallo, H.Fallon, D.J.Gordon, L.J.Grandi, P.Hobbs, C.I.Hooper-Greenhill, E.Jones, E.J.Law, R.P.Le Gall, A.Lugo, D.Michon, A.Mitchell, D.J.Prinjha, R.K.Sheppard, R.J.Watson, A.J.B.Watson, R.J.

(2016) ACS Med Chem Lett 7: 552

  • DOI: https://doi.org/10.1021/acsmedchemlett.6b00092
  • Primary Citation of Related Structures:  
    5G4R, 5G4S

  • PubMed Abstract: 

    The BRPF (Bromodomain and PHD Finger-containing) protein family are important scaffolding proteins for assembly of MYST histone acetyltransferase complexes. A selective benzimidazolone BRPF1 inhibitor showing micromolar activity in a cellular target engagement assay was recently described. Herein, we report the optimization of this series leading to the identification of a superior BRPF1 inhibitor suitable for in vivo studies.


  • Organizational Affiliation

    Epinova Discovery Performance Unit, Quantitative Pharmacology, Experimental Medicine Unit, Flexible Discovery Unit, and Platform Technology and Science, GlaxoSmithKline , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PEREGRIN118Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8VI
Query on 8VI

Download Ideal Coordinates CCD File 
B [auth A]N-[1,3-dimethyl-6-[(2R)-2-methylpiperazin-1-yl]-2-oxidanylidene-benzimidazol-5-yl]-N-ethyl-2-methoxy-benzamide
C24 H31 N5 O3
WFXIHQFRQPGCCR-MRXNPFEDSA-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
8VI BindingDB:  5G4S IC50: min: 1000, max: 3981 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.53α = 90
b = 60.53β = 90
c = 85.14γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2016-07-06 
  • Deposition Author(s): Chung, C.

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other