6FGV

Crystal Structure of BAZ2A bromodomain in complex with 1-methylpyridinone compound 3

• PDB DOI: https://doi.org/10.2210/pdb6FGV/pdb

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


• Deposited: 2018-01-11 Released: 2018-05-30 
• Deposition Author(s): Dalle Vedove, A., Spiliotopoulos, D., Lolli, G., Caflisch, A.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.266 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 

Starting Model: experimental

Literature

Structural Analysis of Small-Molecule Binding to the BAZ2A and BAZ2B Bromodomains.

Dalle Vedove, A., Spiliotopoulos, D., D'Agostino, V.G., Marchand, J.R., Unzue, A., Nevado, C., Lolli, G., Caflisch, A.

(2018) ChemMedChem 13: 1479-1487

• PubMed: 29770599 
• DOI: https://doi.org/10.1002/cmdc.201800234
• Primary Citation of Related Structures:  
  6FG6, 6FGF, 6FGG, 6FGH, 6FGI, 6FGL, 6FGT, 6FGU, 6FGV, 6FGW, 6FH6, 6FH7


• PubMed Abstract: 
  

  The bromodomain-containing protein BAZ2A is a validated target in prostate cancer research, whereas the function of its paralogue BAZ2B is still undefined. The bromodomains of BAZ2A and BAZ2B have a similar binding site for their natural ligand, the acetylated lysine side chain. Here, we present an analysis of the binding modes of eight compounds belonging to three distinct chemical classes. For all compounds, the moiety mimicking the natural ligand engages in essentially identical interactions in the BAZ2A and BAZ2B bromodomains. In contrast, the rest of the molecule is partially solvent-exposed and adopts different orientations with different interactions in the two bromodomains. Some of these differences could be exploited for designing inhibitors with selectivity within the BAZ2 bromodomain subfamily.

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Organizational Affiliation: 

Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123, Povo-Trento, Italy.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 12.77 kDa 
• Atom Count: 889 
• Modelled Residue Count: 103 
• Deposited Residue Count: 106 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain adjacent to zinc finger domain protein 2A	A	106	Homo sapiens	Mutation(s): 0  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
D9T (Subject of Investigation/LOI)	B [auth A]	~{N}-[(1-azanylcyclohexyl)methyl]-1-methyl-6-oxidanylidene-pyridine-3-carboxamide C14 H21 N3 O2 OYMFRGAWSOVJKP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.266 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.786	α = 90
b = 94.786	β = 90
c = 32.78	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-30 
Deposition Author(s): Dalle Vedove, A., Spiliotopoulos, D., Lolli, G., Caflisch, A.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A_169007

Revision History  

• Version 1.0: 2018-05-30
  Type: Initial release
  
• Version 1.1: 2018-08-29
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description