Crystal Structure of BAZ2B bromodomain in complex with fragment F103

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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High-Throughput Fragment Docking into the BAZ2B Bromodomain: Efficient in Silico Screening for X-Ray Crystallography.

Lolli, G.Caflisch, A.

(2016) ACS Chem Biol 11: 800-807

  • DOI: https://doi.org/10.1021/acschembio.5b00914
  • Primary Citation of Related Structures:  
    5DYU, 5DYX, 5E9I, 5E9K, 5E9L, 5E9M, 5E9Y, 5EA1

  • PubMed Abstract: 

    Bromodomains are protein modules that bind to acetylated lysine side chains in histones and other proteins. The bromodomain adjacent to zinc finger domain protein 2B (BAZ2B) has been reported to be poorly druggable. Here, we screened an in-house library of 350 fragments by automatic docking to the BAZ2B bromodomain. The top 12 fragments according to the predicted binding energy were selected for experiments of soaking into apo crystals of BAZ2B which yielded the structure of the complex for four of them, which is a hit rate of 33%. Additional crystal structures were solved for BAZ2B and two scaffolds identified by analogy. For three topologically similar fragments, the crystal structures reveal binding modes with different penetration, i.e., with zero, one, and two water molecules, respectively, located between the fragment and the side chain of a conserved tyrosine (Tyr1901) in the bottom of the acetyl lysine pocket of BAZ2B. Furthermore, a remarkable stereoselectivity of the acetyl lysine pocket emerges from the crystal structures of the bromodomains of BAZ2B and SMARCA4 in complex with the chiral diol MPD (2-methyl-2,4-pentanediol).

  • Organizational Affiliation

    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 6AI

Download Ideal Coordinates CCD File 
B [auth A]1H-indazol-6-amine
C7 H7 N3
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.919α = 90
b = 96.209β = 90
c = 57.779γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-03-30
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description