4NRC | pdb_00004nrc

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

• PDB DOI: https://doi.org/10.2210/pdb4NRC/pdb

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


• Deposited: 2013-11-26 Released: 2013-12-25 
• Deposition Author(s): Muniz, J.R.C., Felletar, I., Chaikuad, A., Filippakopoulos, P., Ferguson, F.M., Fedorov, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Ciulli, A., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.191 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

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

• PubMed: 24304323 
• DOI: https://doi.org/10.1021/jm401582c
• Primary Citation 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. Our results provide attractive leads for development of BAZ2B chemical probes and indicate the whole family may be tractable.

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Organizational Affiliation: 
• Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge, CB2 1EW, U.K.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.47 kDa 
• Atom Count: 1,216 
• Modeled Residue Count: 115 
• Deposited Residue Count: 117 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain adjacent to zinc finger domain protein 2B	A	117	Homo sapiens	Mutation(s): 0  Gene Names: BAZ2B, KIAA1476
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIF8 (Homo sapiens) Explore Q9UIF8  Go to UniProtKB:  Q9UIF8
PHAROS:  Q9UIF8 GTEx:  ENSG00000123636

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
15P	E [auth A]	POLYETHYLENE GLYCOL (N=34) C69 H140 O35 VUYXVWGKCKTUMF-UHFFFAOYSA-N
2LY	B [auth A]	N-methyl-2,3-dihydrothieno[3,4-b][1,4]dioxine-5-carboxamide C8 H9 N O3 S MXUQWUJJYQPEJH-UHFFFAOYSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2LY	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 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.27	α = 90
b = 96.59	β = 90
c = 57.74	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-25 
Deposition Author(s): Muniz, J.R.C., Felletar, I., Chaikuad, A., Filippakopoulos, P., Ferguson, F.M., Fedorov, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Ciulli, A., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2013-12-25
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description