5TTF

Crystal structure of catalytic domain of G9a with MS012


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Potent and Selective Inhibitors for G9a-Like Protein (GLP) Lysine Methyltransferase.

Xiong, Y.Li, F.Babault, N.Dong, A.Zeng, H.Wu, H.Chen, X.Arrowsmith, C.H.Brown, P.J.Liu, J.Vedadi, M.Jin, J.

(2017) J. Med. Chem. 60: 1876-1891

  • DOI: 10.1021/acs.jmedchem.6b01645
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • G9a-like protein (GLP) and G9a are highly homologous protein lysine methyltransferases (PKMTs) sharing approximately 80% sequence identity in their catalytic domains. GLP and G9a form a heterodimer complex and catalyze mono- and dimethylation of hist ...

    G9a-like protein (GLP) and G9a are highly homologous protein lysine methyltransferases (PKMTs) sharing approximately 80% sequence identity in their catalytic domains. GLP and G9a form a heterodimer complex and catalyze mono- and dimethylation of histone H3 lysine 9 and nonhistone substrates. Although they are closely related, GLP and G9a possess distinct physiological and pathophysiological functions. Thus, GLP or G9a selective small-molecule inhibitors are useful tools to dissect their distinct biological functions. We previously reported potent and selective G9a/GLP dual inhibitors including UNC0638 and UNC0642. Here we report the discovery of potent and selective GLP inhibitors including 4 (MS0124) and 18 (MS012), which are >30-fold and 140-fold selective for GLP over G9a and other methyltransferases, respectively. The cocrystal structures of GLP and G9a in the complex with either 4 or 18 displayed virtually identical binding modes and interactions, highlighting the challenges in structure-based design of selective inhibitors for either enzyme.


    Organizational Affiliation

    Department of Pharmacology and Toxicology, University of Toronto , Toronto, Ontario M5S 1A8, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5G 2M9, Canada.,Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States.,Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase EHMT2
A, B, C, D
283Homo sapiensMutation(s): 0 
Gene Names: EHMT2 (BAT8, C6orf30, G9A, KMT1C, NG36)
EC: 2.1.1.-
Find proteins for Q96KQ7 (Homo sapiens)
Go to Gene View: EHMT2
Go to UniProtKB:  Q96KQ7
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7KZ
Query on 7KZ

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A, B, C, D
N4-(1-methylpiperidin-4-yl)-N2-hexyl-6,7-dimethoxyquinazoline-2,4-diamine
N~2~-hexyl-6,7-dimethoxy-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine
C22 H35 N5 O2
ZYNUWSFRZCRKSN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
UNX
Query on UNX

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A, B, C, D
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
SAM
Query on SAM

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A, B, C, D
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 56.846α = 92.09
b = 67.749β = 90.05
c = 77.845γ = 91.80
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
HKL-3000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2018-05-23
    Type: Data collection, Database references