9F78 | pdb_00009f78

BAZ2A bromodomain in complex with acetylpyrrole derivative compound 28-TN23

• PDB DOI: https://doi.org/10.2210/pdb9F78/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2024-05-03 Released: 2025-05-14 
• Deposition Author(s): Dalle Vedove, A., Cazzanelli, G., Caflisch, A., Lolli, G.
• Funding Organization(s): Italian Association for Cancer Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.252 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Unusual backfolded binding poses of BAZ2A bromodomain binders

Dalle Vedove, A., Cazzanelli, G., D'Agostino, V.G., Caflisch, A., Lolli, G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 25.46 kDa 
• Atom Count: 2,049 
• Modeled Residue Count: 205 
• Deposited Residue Count: 210 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain adjacent to zinc finger domain protein 2A	A, B	105	Homo sapiens	Mutation(s): 1  Gene Names: BAZ2A, KIAA0314, TIP5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIF9 (Homo sapiens) Explore Q9UIF9  Go to UniProtKB:  Q9UIF9
PHAROS:  Q9UIF9 GTEx:  ENSG00000076108

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1H98 (Subject of Investigation/LOI)	C [auth A], D [auth B]	1-[4-ethyl-5-[4-[(5-ethyl-1,2,4-oxadiazol-3-yl)methyl]piperazin-1-yl]carbonyl-2-methyl-1~{H}-pyrrol-3-yl]ethanone C19 H27 N5 O3 AFYXSOFFFMWOFB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.252 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.024	α = 90
b = 54.36	β = 90
c = 90.159	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Dalle Vedove, A., Cazzanelli, G., Caflisch, A., Lolli, G.

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Funding Organization	Location	Grant Number
Italian Association for Cancer Research	Italy	MFAG 2017 - ID. 19882

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release