5FH6

Crystal structure of the fifth bromodomain of human PB1 in complex with compound 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification and Development of 2,3-Dihydropyrrolo[1,2-a]quinazolin-5(1H)-one Inhibitors Targeting Bromodomains within the Switch/Sucrose Nonfermenting Complex.

Sutherell, C.L.Tallant, C.Monteiro, O.P.Yapp, C.Fuchs, J.E.Fedorov, O.Siejka, P.Muller, S.Knapp, S.Brenton, J.D.Brennan, P.E.Ley, S.V.

(2016) J.Med.Chem. 59: 5095-5101

  • DOI: 10.1021/acs.jmedchem.5b01997
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bromodomain containing proteins PB1, SMARCA4, and SMARCA2 are important components of SWI/SNF chromatin remodeling complexes. We identified bromodomain inhibitors that target these proteins and display unusual binding modes involving water displaceme ...

    Bromodomain containing proteins PB1, SMARCA4, and SMARCA2 are important components of SWI/SNF chromatin remodeling complexes. We identified bromodomain inhibitors that target these proteins and display unusual binding modes involving water displacement from the KAc binding site. The best compound binds the fifth bromodomain of PB1 with a KD of 124 nM, SMARCA2B and SMARCA4 with KD values of 262 and 417 nM, respectively, and displays excellent selectivity over bromodomains other than PB1, SMARCA2, and SMARCA4.


    Organizational Affiliation

    Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge, CB2 1EW, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein polybromo-1
A, B, C, D
124Homo sapiensMutation(s): 0 
Gene Names: PBRM1 (BAF180, PB1)
Find proteins for Q86U86 (Homo sapiens)
Go to Gene View: PBRM1
Go to UniProtKB:  Q86U86
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5XM
Query on 5XM

Download SDF File 
Download CCD File 
A, B, C, D
(3~{R})-3-(piperidin-1-ylmethyl)-2,3-dihydro-1~{H}-pyrrolo[1,2-a]quinazolin-5-one
C17 H21 N3 O
CDOMBRFDONICCK-CYBMUJFWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.254 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.871α = 90.00
b = 136.416β = 92.33
c = 56.752γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-06-08
    Type: Database references