5E74

Crystal Structure of BAZ2B bromodomain in complex with acetylindole compound UZH50

• PDB DOI: https://doi.org/10.2210/pdb5E74/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-10-11 Released: 2015-10-21 
• Deposition Author(s): Lolli, G., Spiliotopoulos, D., Dolbois, A., Nevado, C., Caflisch, A.
• Funding Organization(s): Swiss Cancer Society (Krebsliga), Swiss National Science Foundation

---

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 

Starting Model: experimental

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

• PubMed: 26982797 
• 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 13.98 kDa 
• Atom Count: 1,107 
• Modelled Residue Count: 116 
• Deposited Residue Count: 116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain adjacent to zinc finger domain protein 2B	A	116	Homo sapiens	Mutation(s): 0  Gene Names: BAZ2B, KIAA1476
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIF8 (Homo sapiens) Explore Q9UIF8  Go to UniProtKB:  Q9UIF8
PHAROS:  Q9UIF8 GTEx:  ENSG00000123636

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5KH	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

Binding Affinity Annotations
ID	Source	Binding Affinity
5KH	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: https://doi.org/10.15785/SBGRID/257

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.649	α = 90
b = 96.58	β = 90
c = 57.914	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-10-21 
Deposition Author(s): Lolli, G., Spiliotopoulos, D., Dolbois, A., Nevado, C., Caflisch, A.

---

Funding Organization	Location	Grant Number
Swiss Cancer Society (Krebsliga)	Switzerland	--
Swiss National Science Foundation	Switzerland	--

Revision History  

• Version 1.0: 2015-10-21
  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