5L98

Crystal Structure of BAZ2B bromodomain in complex with 3-amino-2-methylpyridine derivative 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.263 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1021/acs.jmedchem.6b01258
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain adjacent to zinc finger domain protein 2B
A
116Homo sapiensMutation(s): 0 
Gene Names: BAZ2B (KIAA1476)
Find proteins for Q9UIF8 (Homo sapiens)
Go to Gene View: BAZ2B
Go to UniProtKB:  Q9UIF8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
6RY
Query on 6RY

Download SDF File 
Download CCD File 
A
~{N}-[(1~{S})-1-(2,3-dihydro-1,4-benzodioxin-6-yl)ethyl]-2-methyl-pyridin-3-amine
C16 H18 N2 O2
UFPSUOFEQKCPHZ-NSHDSACASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.263 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.204 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 80.503α = 90.00
b = 96.394β = 90.00
c = 57.613γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--
Swiss Cancer LeagueSwitzerland--

Revision History 

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