5MYG

Crystal structure of the bromodomain of human BRPF1 in complex with NI-57 chemical probe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Design of a Chemical Probe for the Bromodomain and Plant Homeodomain Finger-Containing (BRPF) Family of Proteins.

Igoe, N.Bayle, E.D.Tallant, C.Fedorov, O.Meier, J.C.Savitsky, P.Rogers, C.Morias, Y.Scholze, S.Boyd, H.Cunoosamy, D.Andrews, D.M.Cheasty, A.Brennan, P.E.Muller, S.Knapp, S.Fish, P.V.

(2017) J Med Chem 60: 6998-7011

  • DOI: 10.1021/acs.jmedchem.7b00611
  • Primary Citation of Related Structures:  
    5MYG

  • PubMed Abstract: 
  • The bromodomain and plant homeodomain finger-containing (BRPF) family are scaffolding proteins important for the recruitment of histone acetyltransferases of the MYST family to chromatin. Here, we describe NI-57 (16) as new pan-BRPF chemical probe of the bromodomain (BRD) of the BRPFs ...

    The bromodomain and plant homeodomain finger-containing (BRPF) family are scaffolding proteins important for the recruitment of histone acetyltransferases of the MYST family to chromatin. Here, we describe NI-57 (16) as new pan-BRPF chemical probe of the bromodomain (BRD) of the BRPFs. Inhibitor 16 preferentially bound the BRD of BRPF1 and BRPF2 over BRPF3, whereas binding to BRD9 was weaker. Compound 16 has excellent selectivity over nonclass IV BRD proteins. Target engagement of BRPF1B and BRPF2 with 16 was demonstrated in nanoBRET and FRAP assays. The binding of 16 to BRPF1B was rationalized through an X-ray cocrystal structure determination, which showed a flipped binding orientation when compared to previous structures. We report studies that show 16 has functional activity in cellular assays by modulation of the phenotype at low micromolar concentrations in both cancer and inflammatory models. Pharmacokinetic data for 16 was generated in mouse with single dose administration showing favorable oral bioavailability.


    Organizational Affiliation

    UCL School of Pharmacy, University College London , 29/39 Brunswick Square, London WC1N 1AX, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PeregrinA, B, C, D116Homo sapiensMutation(s): 0 
Gene Names: BRPF1BR140
UniProt & NIH Common Fund Data Resources
Find proteins for P55201 (Homo sapiens)
Explore P55201 
Go to UniProtKB:  P55201
PHAROS:  P55201
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LS8
Query on LS8

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C], H [auth D]4-cyano-~{N}-(1,3-dimethyl-2-oxidanylidene-quinolin-6-yl)-2-methoxy-benzenesulfonamide
C19 H17 N3 O4 S
UEMQPCYDWCSVCU-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LS8Kd:  31   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.14α = 90
b = 123.716β = 90
c = 137.073γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Database references