6AU2 | pdb_00006au2

Crystal structure of SETDB1 Tudor domain with aryl triazole fragments

• PDB DOI: https://doi.org/10.2210/pdb6AU2/pdb

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


• Deposited: 2017-08-30 Released: 2017-10-11 
• Deposition Author(s): MADER, P., Mendoza-Sanchez, R., IQBAL, A., DONG, A., DOBROVETSKY, E., CORLESS, V.B., LIEW, S.K., TEMPEL, W., SMIL, D., DELA SENA, C.C., KENNEDY, S., DIAZ, D., HOLOWNIA, A., VEDADI, M., BROWN, P.J., SANTHAKUMAR, V., Bountra, C., Edwards, A.M., YUDIN, A.K., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.208 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

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

• PubMed: 31327677 
• DOI: https://doi.org/10.1016/j.bmc.2019.07.020
• Primary Citation 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 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.

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Organizational Affiliation: 
• Structural Genomics Consortium, University of Toronto, Toronto, Canada.
Department of Chemistry, University of Toronto, Toronto, Canada.
Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Canada.
Structural Genomics Consortium, University of Toronto, Toronto, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada.
Department of Chemistry, University of Toronto, Toronto, Canada. Electronic address: [e-mail].
Structural Genomics Consortium, University of Toronto, Toronto, Canada; Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Canada. Electronic address: [e-mail].

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: 26.1 kDa 
• Atom Count: 2,058 
• Modeled Residue Count: 210 
• Deposited Residue Count: 213 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SETDB1	A	213	Homo sapiens	Mutation(s): 0  Gene Names: SETDB1, KIAA0067, KMT1E EC: 2.1.1.43 (PDB Primary Data), 2.1.1.366 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q15047 (Homo sapiens) Explore Q15047  Go to UniProtKB:  Q15047
PHAROS:  Q15047 GTEx:  ENSG00000143379

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CGJ	B [auth A]	1-methyl-4H,6H-[1,2,4]triazolo[4,3-a][4,1]benzoxazepine C11 H11 N3 O HEEIZXCFEVISIX-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BME	C [auth A], D [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
EDO	J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNX	AA [auth A], BA [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.208 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.202	α = 90
b = 63.273	β = 90
c = 69.859	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-11 
Deposition Author(s): MADER, P., Mendoza-Sanchez, R., IQBAL, A., DONG, A., DOBROVETSKY, E., CORLESS, V.B., LIEW, S.K., TEMPEL, W., SMIL, D., DELA SENA, C.C., KENNEDY, S., DIAZ, D., HOLOWNIA, A., VEDADI, M., BROWN, P.J., SANTHAKUMAR, V., Bountra, C., Edwards, A.M., YUDIN, A.K., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2017-10-11
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection, Database references
• Version 1.2: 2025-04-02
  Changes: Data collection, Database references, Structure summary