3RJW

Crystal structure of histone lysine methyltransferase g9a with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells.

Vedadi, M.Barsyte-Lovejoy, D.Liu, F.Rival-Gervier, S.Allali-Hassani, A.Labrie, V.Wigle, T.J.Dimaggio, P.A.Wasney, G.A.Siarheyeva, A.Dong, A.Tempel, W.Wang, S.C.Chen, X.Chau, I.Mangano, T.J.Huang, X.P.Simpson, C.D.Pattenden, S.G.Norris, J.L.Kireev, D.B.Tripathy, A.Edwards, A.Roth, B.L.Janzen, W.P.Garcia, B.A.Petronis, A.Ellis, J.Brown, P.J.Frye, S.V.Arrowsmith, C.H.Jin, J.

(2011) Nat Chem Biol 7: 566-574

  • DOI: 10.1038/nchembio.599
  • Primary Citation of Related Structures:  
    3RJW

  • PubMed Abstract: 
  • Protein lysine methyltransferases G9a and GLP modulate the transcriptional repression of a variety of genes via dimethylation of Lys9 on histone H3 (H3K9me2) as well as dimethylation of non-histone targets. Here we report the discovery of UNC0638, an inhibitor of G9a and GLP with excellent potency and selectivity over a wide range of epigenetic and non-epigenetic targets ...

    Protein lysine methyltransferases G9a and GLP modulate the transcriptional repression of a variety of genes via dimethylation of Lys9 on histone H3 (H3K9me2) as well as dimethylation of non-histone targets. Here we report the discovery of UNC0638, an inhibitor of G9a and GLP with excellent potency and selectivity over a wide range of epigenetic and non-epigenetic targets. UNC0638 treatment of a variety of cell lines resulted in lower global H3K9me2 levels, equivalent to levels observed for small hairpin RNA knockdown of G9a and GLP with the functional potency of UNC0638 being well separated from its toxicity. UNC0638 markedly reduced the clonogenicity of MCF7 cells, reduced the abundance of H3K9me2 marks at promoters of known G9a-regulated endogenous genes and disproportionately affected several genomic loci encoding microRNAs. In mouse embryonic stem cells, UNC0638 reactivated G9a-silenced genes and a retroviral reporter gene in a concentration-dependent manner without promoting differentiation.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase EHMT2A, B283Homo sapiensMutation(s): 0 
Gene Names: EHMT2BAT8C6orf30G9AKMT1CNG36
EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96KQ7 (Homo sapiens)
Explore Q96KQ7 
Go to UniProtKB:  Q96KQ7
PHAROS:  Q96KQ7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIQ (Subject of Investigation/LOI)
Query on CIQ

Download Ideal Coordinates CCD File 
DA [auth B], H [auth A]2-cyclohexyl-6-methoxy-N-[1-(1-methylethyl)piperidin-4-yl]-7-(3-pyrrolidin-1-ylpropoxy)quinazolin-4-amine
C30 H47 N5 O2
QOECJCJVIMVJGX-UHFFFAOYSA-N
 Ligand Interaction
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
CA [auth B], G [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth B], BA [auth B], C [auth A], D [auth A], E [auth A], F [auth A], Y [auth B], Z [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
EA [auth B] , FA [auth B] , GA [auth B] , HA [auth B] , I [auth A] , IA [auth B] , J [auth A] , JA [auth B] , 
EA [auth B],  FA [auth B],  GA [auth B],  HA [auth B],  I [auth A],  IA [auth B],  J [auth A],  JA [auth B],  K [auth A],  KA [auth B],  L [auth A],  LA [auth B],  M [auth A],  MA [auth B],  N [auth A],  NA [auth B],  O [auth A],  OA [auth B],  P [auth A],  PA [auth B],  Q [auth A],  QA [auth B],  R [auth A],  S [auth A],  T [auth A],  U [auth A],  V [auth A],  W [auth A],  X [auth A]
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CIQ BindingDB:  3RJW Ki: 3.7 (nM) from 1 assay(s)
Kd: 1420 (nM) from 1 assay(s)
IC50: min: 2.5, max: 610 (nM) from 16 assay(s)
PDBBind:  3RJW Kd: 27 (nM) from 1 assay(s)
SAH BindingDB:  3RJW Ki: 570 (nM) from 1 assay(s)
IC50: min: 2000, max: 4100 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.58α = 90
b = 78.083β = 92.16
c = 70.252γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-07-20
    Changes: Other
  • Version 1.3: 2011-08-03
    Changes: Database references
  • Version 1.4: 2017-11-08
    Changes: Refinement description