6AU2

Crystal structure of SETDB1 Tudor domain with aryl triazole fragments


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification and characterization of the first fragment hits for SETDB1 Tudor domain.

Mader, P.Mendoza-Sanchez, R.Iqbal, A.Dong, A.Dobrovetsky, E.Corless, V.B.Liew, S.K.Houliston, S.R.De Freitas, R.F.Smil, D.Sena, C.C.D.Kennedy, S.Diaz, D.B.Wu, H.Dombrovski, L.Allali-Hassani, A.Min, J.Schapira, M.Vedadi, M.Brown, P.J.Santhakumar, V.Yudin, A.K.Arrowsmith, C.H.

(2019) Bioorg Med Chem 27: 3866-3878

  • DOI: 10.1016/j.bmc.2019.07.020
  • Primary Citation of Related Structures:  
    6AU2

  • PubMed Abstract: 
  • SET domain bifurcated protein 1 (SETDB1) is a human histone-lysine methyltransferase which is amplified in human cancers and was shown to be crucial in the growth of non-small and small cell lung carcinoma. In addition to its catalytic domain, SETDB1 har ...

    SET domain bifurcated protein 1 (SETDB1) is a human histone-lysine methyltransferase which is amplified in human cancers and was shown to be crucial in the growth of non-small and small cell lung carcinoma. In addition to its catalytic domain, SETDB1 harbors a unique tandem tudor domain which recognizes histone sequences containing both methylated and acetylated lysines, and likely contributes to its localization on chromatin. Using X-ray crystallography and NMR spectroscopy fragment screening approaches, we have identified the first small molecule fragment hits that bind to histone peptide binding groove of the Tandem Tudor Domain (TTD) of SETDB1. Herein, we describe the binding modes of these fragments and analogues and the biophysical characterization of key compounds. These confirmed small molecule fragments will inform the development of potent antagonists of SETDB1 interaction with histones.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, Canada; Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Canada. Electronic address: Cheryl.Arrowsmith@uhnresearch.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SETDB1 A213Homo sapiensMutation(s): 0 
Gene Names: SETDB1KIAA0067KMT1EESET
EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt)
Find proteins for Q15047 (Homo sapiens)
Explore Q15047 
Go to UniProtKB:  Q15047
NIH Common Fund Data Resources
PHAROS:  Q15047
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CGJ
Query on CGJ

Download Ideal Coordinates CCD File 
A
1-methyl-4H,6H-[1,2,4]triazolo[4,3-a][4,1]benzoxazepine
C11 H11 N3 O
HEEIZXCFEVISIX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BME
Query on BME

Download Ideal Coordinates CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
A
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.202α = 90
b = 63.273β = 90
c = 69.859γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building
HKL-3000data reduction

Structure Validation

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Entry History 

Revision History 

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references