5OR8

Crystal Structure of BAZ2A bromodomain in complex with 1,3-dimethyl-benzimidazolone compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking.

Marchand, J.R.Dalle Vedove, A.Lolli, G.Caflisch, A.

(2017) J Chem Inf Model 57: 2584-2597

  • DOI: 10.1021/acs.jcim.7b00336
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The high-throughput docking protocol called ALTA-VS (anchor-based library tailoring approach for virtual screening) was developed in 2005 for the efficient in silico screening of large libraries of compounds by preselection of only those molecules th ...

    The high-throughput docking protocol called ALTA-VS (anchor-based library tailoring approach for virtual screening) was developed in 2005 for the efficient in silico screening of large libraries of compounds by preselection of only those molecules that have optimal fragments (anchors) for the protein target. Here we present an updated version of ALTA-VS with a broader range of potential applications. The evaluation of binding energy makes use of a classical force field with implicit solvent in the continuum dielectric approximation. In about 2 days per protein target on a 96-core compute cluster (equipped with Xeon E3-1280 quad core processors at 2.5 GHz), the screening of a library of nearly 77 000 diverse molecules with the updated ALTA-VS protocol has resulted in the identification of 19, 3, 3, and 2 μM inhibitors of the human bromodomains ATAD2, BAZ2B, BRD4(1), and CREBBP, respectively. The success ratio (i.e., number of actives in a competition binding assay in vitro divided by the number of compounds tested) ranges from 8% to 13% in dose-response measurements. The poses predicted by fragment-based docking for the three ligands of the BAZ2B bromodomain were confirmed by protein X-ray crystallography.


    Organizational Affiliation

    Department of Biochemistry, University of Zürich , CH-8057, Zürich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain adjacent to zinc finger domain protein 2A
A
106Homo sapiensMutation(s): 0 
Gene Names: BAZ2A (KIAA0314, TIP5)
Find proteins for Q9UIF9 (Homo sapiens)
Go to Gene View: BAZ2A
Go to UniProtKB:  Q9UIF9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JR4
Query on JR4

Download SDF File 
Download CCD File 
A
~{N}-[(4-fluorophenyl)methyl]-1,3,6-trimethyl-2-oxidanylidene-benzimidazole-5-sulfonamide
C17 H18 F N3 O3 S
HJRSXSGULYKETP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 95.136α = 90.00
b = 95.136β = 90.00
c = 32.653γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss Cancer Society (Krebsliga Schweiz)SwitzerlandKLS-3098- 02-2013

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Database references