5TTG | pdb_00005ttg

Crystal structure of catalytic domain of GLP with MS012

• PDB DOI: https://doi.org/10.2210/pdb5TTG/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2016-11-03 Released: 2017-02-01 
• Deposition Author(s): DONG, A., ZENG, H., LIU, J., XIONG, Y., BABAULT, N., JIN, J., TEMPEL, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., WU, H., BROWN, P.J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.192 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

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

• PubMed: 28135087 
• DOI: https://doi.org/10.1021/acs.jmedchem.6b01645
• Primary Citation Related Structures: 
  5TTF, 5TTG, 5TUY, 5TUZ


• 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 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.

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Organizational Affiliation: 
• 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.
Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5G 2M9, Canada.
Department of Pharmacology and Toxicology, University of Toronto , Toronto, Ontario M5S 1A8, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 68.28 kDa 
• Atom Count: 5,119 
• Modeled Residue Count: 518 
• Deposited Residue Count: 574 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase EHMT1	A, B	287	Homo sapiens	Mutation(s): 0  Gene Names: EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D EC: 2.1.1 (PDB Primary Data), 2.1.1.43 (PDB Primary Data), 2.1.1.367 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9B1 (Homo sapiens) Explore Q9H9B1  Go to UniProtKB:  Q9H9B1
PHAROS:  Q9H9B1 GTEx:  ENSG00000181090

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7KZ	D [auth A], R [auth B]	N4-(1-methylpiperidin-4-yl)-N2-hexyl-6,7-dimethoxyquinazoline-2,4-diamine C22 H35 N5 O2 ZYNUWSFRZCRKSN-UHFFFAOYSA-N
SAM	C [auth A], Q [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
GOL	J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	W [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	E [auth A], F [auth A], G [auth A], H [auth A], S [auth B], T [auth B], U [auth B], V [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNX	AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], X [auth B], Y [auth B], Z [auth B]	UNKNOWN ATOM OR ION X

Binding Affinity Annotations
ID	Source	Binding Affinity
7KZ	BindingDB:  5TTG	Kd: 46 (nM) from 1 assay(s)
		IC50: 7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.192 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35ttg

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.429	α = 90
b = 95.9	β = 90
c = 102.113	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): DONG, A., ZENG, H., LIU, J., XIONG, Y., BABAULT, N., JIN, J., TEMPEL, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., WU, H., BROWN, P.J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2018-05-23
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description