7T7L | pdb_00007t7l

Structure of human G9a SET-domain (EHMT2) in complex with covalent inhibitor (Compound 1)

PDB DOI: https://doi.org/10.2210/pdb7T7L/pdb

Classification: GENE REGULATION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-12-15 Released: 2022-07-06
Deposition Author(s): Park, K.-S., Kumar, P.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.251 (Depositor), 0.253 (DCC)
R-Value Work:
0.204 (Depositor), 0.208 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Discovery of the First-in-Class G9a/GLP Covalent Inhibitors.

Park, K.S., Xiong, Y., Yim, H., Velez, J., Babault, N., Kumar, P., Liu, J., Jin, J.

(2022) J Med Chem 65: 10506-10522

PubMed: 35763668 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.2c00652
Primary Citation Related Structures:
7T7L, 7T7M

PubMed Abstract:
The highly homologous protein lysine methyltransferases G9a and GLP, which catalyze mono- and dimethylation of histone H3 lysine 9 (H3K9), have been implicated in various human diseases. To investigate functions of G9a and GLP in human diseases, we and others reported several noncovalent reversible small-molecule inhibitors of G9a and GLP. Here, we report the discovery of the first-in-class G9a/GLP covalent irreversible inhibitors, 1 and 8 (MS8511), by targeting a cysteine residue at the substrate binding site. We characterized these covalent inhibitors in enzymatic, mass spectrometry based and cellular assays and using X-ray crystallography. Compared to the noncovalent G9a/GLP inhibitor UNC0642, covalent inhibitor 8 displayed improved potency in enzymatic and cellular assays. Interestingly, compound 8 also displayed potential kinetic preference for covalently modifying G9a over GLP. Collectively, compound 8 could be a useful chemical tool for studying the functional roles of G9a and GLP by covalently modifying and inhibiting these methyltransferases.

Organizational Affiliation

Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States.

Macromolecule Content

Total Structure Weight: 135.05 kDa
Atom Count: 9,210
Modeled Residue Count: 1,065
Deposited Residue Count: 1,132
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase EHMT2	A, B, C, D	283	Homo sapiens	Mutation(s): 0 Gene Names: EHMT2, BAT8, C6orf30, G9A, KMT1C, NG36 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 Q96KQ7 (Homo sapiens) Explore Q96KQ7 Go to UniProtKB: Q96KQ7
PHAROS: Q96KQ7 GTEx: ENSG00000204371
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96KQ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G5U (Subject of Investigation/LOI) Query on G5U Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain J [auth A] SDF format, chain BA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain J [auth A] mmCIF format, chain BA [auth D]	BA [auth D], J [auth A], P [auth B]	N-(6-methoxy-4-{[1-(propan-2-yl)piperidin-4-yl]amino}-7-[3-(pyrrolidin-1-yl)propoxy]quinazolin-2-yl)propanamide C₂₇ H₄₂ N₆ O₃ GCPRIPZOIVSIDT-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain J [auth A] Focus chain P [auth B] Interactions & Density Focus chain BA [auth D] Focus chain J [auth A] Focus chain P [auth B]
G4R (Subject of Investigation/LOI) Query on G4R Download:Ideal Coordinates CCD File SDF format, chain V [auth C] MOL2 format, chain V [auth C] mmCIF format, chain V [auth C]	V [auth C]	N-(6-methoxy-4-{[1-(propan-2-yl)piperidin-4-yl]amino}-7-[3-(pyrrolidin-1-yl)propoxy]quinazolin-2-yl)prop-2-enamide C₂₇ H₄₀ N₆ O₃ JBMUWBUCVSKHLE-UHFFFAOYSA-N		Interactions Focus chain V [auth C] Interactions & Density Focus chain V [auth C]
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain U [auth C] SDF format, chain O [auth B] SDF format, chain AA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain U [auth C] MOL2 format, chain O [auth B] MOL2 format, chain AA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain U [auth C] mmCIF format, chain O [auth B] mmCIF format, chain AA [auth D]	AA [auth D], I [auth A], O [auth B], U [auth C]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain AA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain T [auth C] SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] K [auth B] E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], W [auth D], X [auth D], Y [auth D], Z [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]