5CQA

Crystal structure of the bromodomain of bromodomain adjacent to zinc finger domain protein 2B (BAZ2B) in complex with N-methyl-2,3-dihydrothieno[3,4-b][1,4]dioxine-5-carboxamide (SGC - Diamond I04-1 fragment screening)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Crystal structure of the second bromodomain of bromodomain adjancent to zinc finger domain protein 2B (BAZ2B) in complex with N-methyl-2,3-dihydrothieno[3,4-b][1,4]dioxine-5-carboxamide (SGC - Diamond I04-1 fragment screening)

Bradley, A., Pearce, N., Krojer, T., Ng, J., Talon, R., Vollmar, M., Jose, B., von Delft, F., Bountra, C., Arrowsmith, C.H., Edwards, A., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain adjacent to zinc finger domain protein 2B115Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UIF8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2LY
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
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
2LY BindingDB:  5CQA IC50: 2.41e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.16α = 90
b = 96.94β = 90
c = 58.11γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references