Crystal structure of histone lysine methyltransferase g9a with an inhibitor

Experimental Data Snapshot

  • 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 1.5 of the entry. See complete history


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: https://doi.org/10.1038/nchembio.599
  • Primary Citation of Related Structures:  

  • 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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase EHMT2
A, B
283Homo sapiensMutation(s): 0 
Gene Names: EHMT2BAT8C6orf30G9AKMT1CNG36
UniProt & NIH Common Fund Data Resources
Find proteins for Q96KQ7 (Homo sapiens)
Explore Q96KQ7 
Go to UniProtKB:  Q96KQ7
GTEx:  ENSG00000204371 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96KQ7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CIQ

Download Ideal Coordinates CCD File 
DA [auth B],
H [auth A]
C30 H47 N5 O2
Query on SAH

Download Ideal Coordinates CCD File 
CA [auth B],
G [auth A]
C14 H20 N6 O5 S
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
C [auth A]
D [auth A]
E [auth A]
AA [auth B],
BA [auth B],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
Y [auth B],
Z [auth B]
Query on UNX

Download Ideal Coordinates CCD File 
EA [auth B]
FA [auth B]
GA [auth B]
HA [auth B]
I [auth A]
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]
Binding Affinity Annotations 
IDSourceBinding Affinity
SAH BindingDB:  3RJW Ki: 570 (nM) from 1 assay(s)
IC50: min: 1820, max: 4100 (nM) from 3 assay(s)
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)
Experimental Data & Validation

Experimental Data

  • 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
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

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
  • Version 1.5: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description