7BL9

BAZ2A bromodomain in complex with GSK2801 chemical probe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Chemical probes in the BAZ2A bromodomain

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain adjacent to zinc finger domain protein 2A105Homo sapiensMutation(s): 0 
Gene Names: BAZ2AKIAA0314TIP5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIF9 (Homo sapiens)
Explore Q9UIF9 
Go to UniProtKB:  Q9UIF9
PHAROS:  Q9UIF9
GTEx:  ENSG00000076108 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UIF9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3WQ (Subject of Investigation/LOI)
Query on 3WQ

Download Ideal Coordinates CCD File 
B [auth A]1-{1-[2-(methylsulfonyl)phenyl]-7-propoxyindolizin-3-yl}ethanone
C20 H21 N O4 S
KHWCPNJRJCNVRI-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
3WQ BindingDB:  7BL9 Kd: min: 257, max: 3162 (nM) from 2 assay(s)
IC50: 400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.271α = 90
b = 56.802β = 90
c = 76.623γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
Aimlessdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItalyMFAG 2017 - ID. 19882
Swiss National Science FoundationSwitzerlandSNSF grant 310030B-189363

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description