7QYT

BAZ2A bromodomain in complex with acetylpyrrole derivative compound 80


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Identification of a BAZ2A-Bromodomain Hit Compound by Fragment Growing.

Dalle Vedove, A.Cazzanelli, G.Batiste, L.Marchand, J.R.Spiliotopoulos, D.Corsi, J.D'Agostino, V.G.Caflisch, A.Lolli, G.

(2022) ACS Med Chem Lett 13: 1434-1443

  • DOI: 10.1021/acsmedchemlett.2c00173
  • Primary Citation of Related Structures:  
    7B7B, 7B7G, 7B7I, 7B82, 7BC2, 7QVT, 7QVU, 7QVV, 7QWF, 7QWU, 7QWY, 7QX2, 7QX9, 7QXL, 7QYE, 7QYO, 7QYT, 7QYU, 7QYV, 7QYW, 7QZ0, 7QZ4, 7QZB, 7QZC, 7QZI, 7QZT, 7R01, 7R0B

  • PubMed Abstract: 
  • BAZ2A is an epigenetic regulator affecting transcription of ribosomal RNA. It is overexpressed in aggressive and recurrent prostate cancer, promoting cellular migration. Its bromodomain is characterized by a shallow and difficult-to-drug pocket. Here, we describe a structure-based fragment-growing campaign for the identification of ligands of the BAZ2A bromodomain ...

    BAZ2A is an epigenetic regulator affecting transcription of ribosomal RNA. It is overexpressed in aggressive and recurrent prostate cancer, promoting cellular migration. Its bromodomain is characterized by a shallow and difficult-to-drug pocket. Here, we describe a structure-based fragment-growing campaign for the identification of ligands of the BAZ2A bromodomain. By combining docking, competition binding assays, and protein crystallography, we have extensively explored the interactions of the ligands with the rim of the binding pocket, and in particular ionic interactions with the side chain of Glu1820, which is unique to BAZ2A. We present 23 high-resolution crystal structures of the holo BAZ2A bromodomain and analyze common bromodomain/ligand motifs and favorable intraligand interactions. Binding of some of the compounds is enantiospecific, with affinity in the low micromolar range. The most potent ligand has an equilibrium dissociation constant of 7 μM and a good selectivity over the paralog BAZ2B bromodomain.


    Organizational Affiliation

    Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, via Sommarive 9, 38123 Povo - Trento, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain adjacent to zinc finger domain protein 2AA105Homo sapiensMutation(s): 2 
Gene Names: BAZ2AKIAA0314TIP5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIF9 (Homo sapiens)
Explore Q9UIF9 
Go to UniProtKB:  Q9UIF9
PHAROS:  Q9UIF9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UIF9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GJI (Subject of Investigation/LOI)
Query on GJI

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
3-methyl-1-(2-piperazin-1-yl-1,3-thiazol-4-yl)-2,5,6,7-tetrahydroisoindol-4-one
C16 H20 N4 O S
HRDOIKMHSZXEOA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.996α = 90
b = 93.996β = 90
c = 33.075γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItalyMFAG 2017 - ID. 19882

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release