Crystal Structure of BAZ2B bromodomain in complex with acetylindole compound UZH47

Experimental Data Snapshot

  • Resolution: 1.71 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

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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: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain adjacent to zinc finger domain protein 2B116Homo sapiensMutation(s): 0 
Gene Names: BAZ2BKIAA1476
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIF8 (Homo sapiens)
Explore Q9UIF8 
Go to UniProtKB:  Q9UIF8
GTEx:  ENSG00000123636 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UIF8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on UO1

Download Ideal Coordinates CCD File 
B [auth A]N-(1-acetyl-1H-indol-3-yl)-N-(5-hydroxy-2-methylphenyl)acetamide
C19 H18 N2 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
UO1 Binding MOAD:  5E73 Kd: 2.30e+4 (nM) from 1 assay(s)
BindingDB:  5E73 Kd: 2.30e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.175α = 90
b = 96.477β = 90
c = 57.727γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
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: 2015-10-28
    Type: Initial release
  • Version 1.1: 2017-05-03
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description