5E74

Crystal Structure of BAZ2B bromodomain in complex with acetylindole compound UZH50


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The "Gatekeeper" Residue Influences the Mode of Binding of Acetyl Indoles to Bromodomains.

Unzue, A.Zhao, H.Lolli, G.Dong, J.Zhu, J.Zechner, M.Dolbois, A.Caflisch, A.Nevado, C.

(2016) J Med Chem 59: 3087-3097

  • DOI: 10.1021/acs.jmedchem.5b01757
  • Primary Citation of Related Structures:  
    5D7X, 5E73, 5E74

  • PubMed Abstract: 
  • Small-molecule hits for the bromodomains of CREBBP and BAZ2B have been identified by scaffold hopping followed by docking of a set of ∼200 compounds containing the acetyl indole scaffold. Chemical synthesis of nearly 30 derivatives has resulted in ligands of representatives of three subfamilies of human bromodomains with favorable ligand efficiency ...

    Small-molecule hits for the bromodomains of CREBBP and BAZ2B have been identified by scaffold hopping followed by docking of a set of ∼200 compounds containing the acetyl indole scaffold. Chemical synthesis of nearly 30 derivatives has resulted in ligands of representatives of three subfamilies of human bromodomains with favorable ligand efficiency. The X-ray crystal structures of three different bromodomains (CREBBP, BAZ2B, and BRPF1b) in complex with acetyl indole derivatives reveal the influence of the gatekeeper residue on the orientation of small-molecule ligands in the acetyl lysine binding site.


    Organizational Affiliation

    Department of Chemistry and ‡Department of Biochemistry, University of Zürich , Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain adjacent to zinc finger domain protein 2BA116Homo sapiensMutation(s): 0 
Gene Names: BAZ2BKIAA1476
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIF8 (Homo sapiens)
Explore Q9UIF8 
Go to UniProtKB:  Q9UIF8
PHAROS:  Q9UIF8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5KH (Subject of Investigation/LOI)
Query on 5KH

Download Ideal Coordinates CCD File 
B [auth A]N-(1-acetyl-1H-indol-3-yl)-N-(5-hydroxy-2-methylphenyl)-3-(trifluoromethyl)benzamide
C25 H19 F3 N2 O3
GRQZQCNAGDASPY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
5KH Binding MOAD:  5E74 Kd: 3.90e+4 (nM) from 1 assay(s)
BindingDB:  5E74 Kd: 3.90e+4 (nM) from 1 assay(s)
IC50: 2.70e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: C 2 2 21
  • Diffraction Data DOI: 10.15785/SBGRID/257 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.649α = 90
b = 96.58β = 90
c = 57.914γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss Cancer Society (Krebsliga)Switzerland--
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2017-05-03
    Changes: Database references