4NRC

Crystal Structure of the bromodomain of human BAZ2B in complex with compound-3 N01186


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Targeting low-druggability bromodomains: fragment based screening and inhibitor design against the BAZ2B bromodomain.

Ferguson, F.M.Fedorov, O.Chaikuad, A.Philpott, M.Muniz, J.R.Felletar, I.von Delft, F.Heightman, T.Knapp, S.Abell, C.Ciulli, A.

(2013) J Med Chem 56: 10183-10187

  • DOI: 10.1021/jm401582c
  • Primary Citation of Related Structures:  
    4NR9, 4NRA, 4NRB, 4NRC

  • PubMed Abstract: 
  • Bromodomains are epigenetic reader domains that have recently become popular targets. In contrast to BET bromodomains, which have proven druggable, bromodomains from other regions of the phylogenetic tree have shallower pockets. We describe successful targeting of the challenging BAZ2B bromodomain using biophysical fragment screening and structure-based optimization of high ligand-efficiency fragments into a novel series of low-micromolar inhibitors ...

    Bromodomains are epigenetic reader domains that have recently become popular targets. In contrast to BET bromodomains, which have proven druggable, bromodomains from other regions of the phylogenetic tree have shallower pockets. We describe successful targeting of the challenging BAZ2B bromodomain using biophysical fragment screening and structure-based optimization of high ligand-efficiency fragments into a novel series of low-micromolar inhibitors. Our results provide attractive leads for development of BAZ2B chemical probes and indicate the whole family may be tractable.


    Organizational Affiliation

    Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge, CB2 1EW, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain adjacent to zinc finger domain protein 2BA117Homo sapiensMutation(s): 0 
Gene Names: BAZ2BKIAA1476
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIF8 (Homo sapiens)
Explore Q9UIF8 
Go to UniProtKB:  Q9UIF8
PHAROS:  Q9UIF8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
15P
Query on 15P

Download Ideal Coordinates CCD File 
E [auth A]POLYETHYLENE GLYCOL (N=34)
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
 Ligand Interaction
2LY (Subject of Investigation/LOI)
Query on 2LY

Download Ideal Coordinates CCD File 
B [auth A]N-methyl-2,3-dihydrothieno[3,4-b][1,4]dioxine-5-carboxamide
C8 H9 N O3 S
MXUQWUJJYQPEJH-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
2LY Binding MOAD:  4NRC IC50: 2.41e+5 (nM) from 1 assay(s)
BindingDB:  4NRC IC50: 2.41e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.27α = 90
b = 96.59β = 90
c = 57.74γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-25
    Type: Initial release