7BL9

BAZ2A bromodomain in complex with GSK2801 chemical probe

PDB DOI: https://doi.org/10.2210/pdb7BL9/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-01-18 Released: 2022-03-02
Deposition Author(s): Dalle Vedove, A., Cazzanelli, G., Caflisch, A., Lolli, G.
Funding Organization(s): Italian Association for Cancer Research, Swiss National Science Foundation

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.

Macromolecule Content

Total Structure Weight: 12.81 kDa
Atom Count: 1,050
Modelled Residue Count: 105
Deposited Residue Count: 105
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain adjacent to zinc finger domain protein 2A	A	105	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UIF9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3WQ (Subject of Investigation/LOI) Query on 3WQ Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1-{1-[2-(methylsulfonyl)phenyl]-7-propoxyindolizin-3-yl}ethanone C₂₀ H₂₁ N O₄ S KHWCPNJRJCNVRI-UHFFFAOYSA-N		Interactions Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
3WQ	BindingDB: 7BL9	Kd: min: 257, max: 3162 (nM) from 2 assay(s)
3WQ	BindingDB: 7BL9	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 = 44.271	α = 90
b = 56.802	β = 90
c = 76.623	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-03-02

Deposition Author(s):

Dalle Vedove, A.

Funding Organization	Location	Grant Number
Italian Association for Cancer Research	Italy	MFAG 2017 - ID. 19882
Swiss National Science Foundation	Switzerland	SNSF 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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.