Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 13.82 kDa 
• Atom Count: 1042 
• Modelled Residue Count: 116 
• Deposited Residue Count: 116 
• Unique protein chains: 1

5L96

Crystal Structure of BAZ2B bromodomain in complex with 3-amino-2-methylpyridine derivative 1

• PDB DOI: 10.2210/pdb5L96/pdb

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


• Deposited: 2016-06-09 Released: 2016-10-26 
• Deposition Author(s): Lolli, G., Marchand, J.-R., Caflisch, A.
• Funding Organization(s): Swiss National Science Foundation, Swiss Cancer League

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.228 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Derivatives of 3-Amino-2-methylpyridine as BAZ2B Bromodomain Ligands: In Silico Discovery and in Crystallo Validation.

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

(2016) J Med Chem 59: 9919-9927

• PubMed: 27731638 
• DOI: 10.1021/acs.jmedchem.6b01258
• Primary Citation of Related Structures:  
  5L8T, 5L8U, 5L96, 5L97, 5L98, 5L99


• PubMed Abstract: 
  

The 3-amino-2-methylpyridine derivative 1 was identified as ligand of the BAZ2B bromodomain by automatic docking of nearly 500 compounds, selected on the basis of previous fragment hits. Hit expansion by two in silico approaches, pharmacophore search followed by docking, and substructure search resulted in five additional ligands. The predicted binding mode of the six 3-amino-2-methylpyridine derivatives was validated by protein crystallography. A small displacement of residues 1894-1899 of the ZA loop is observed for two of the six ligands. In all structures, the pyridine head is involved in a water-mediated hydrogen bond with the side chain of the conserved Tyr1901 while the 3-amino linker acts as hydrogen bond donor for the backbone carbonyl of Pro1888. Heterogeneous orientations are observed for the tail groups (i.e., the 3-amino substituents). The sulfonyl group in the tail of compounds 1 and 2 is involved in a hydrogen bond with the backbone amide of Asn1894.

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Organizational Affiliation: 

Department of Biochemistry, University of Zürich , Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain adjacent to zinc finger domain protein 2B	A	116	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6RZ	B [auth A]	2-methyl-~{N}-[(2~{R})-1-methylsulfonylpropan-2-yl]pyridin-3-amine C10 H16 N2 O2 S HXYSCWJADZACTE-MRVPVSSYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.228 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.884	α = 90
b = 96.805	β = 90
c = 57.901	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-06-09 
• Released Date: 2016-10-26 
Deposition Author(s): Lolli, G., Marchand, J.-R., Caflisch, A.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--
Swiss Cancer League	Switzerland	--

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2016-12-21
  Changes: Database references