7XUD | pdb_00007xud

Structure of G9a in complex with compound 26a

PDB DOI: https://doi.org/10.2210/pdb7XUD/pdb

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

Deposited: 2022-05-18 Released: 2023-03-29
Deposition Author(s): Niwa, H., Shirai, F., Sato, S., Nishigaya, Y., Umehara, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.177 (Depositor), 0.174 (DCC)
R-Value Work:
0.161 (Depositor), 0.158 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9a Inhibitors as Anticancer Agents.

Nishigaya, Y., Takase, S., Sumiya, T., Kikuzato, K., Sato, T., Niwa, H., Sato, S., Nakata, A., Sonoda, T., Hashimoto, N., Namie, R., Honma, T., Umehara, T., Shirouzu, M., Koyama, H., Yoshida, M., Ito, A., Shirai, F.

(2023) J Med Chem 66: 4059-4085

PubMed: 36882960 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.2c02059
Primary Citation Related Structures:
7XUA, 7XUB, 7XUC, 7XUD

PubMed Abstract:
Identification of structurally novel inhibitors of lysine methyltransferase G9a has been a subject of intense research in cancer epigenetics. Starting with the high-throughput screening (HTS) hit rac - 10a obtained from the chemical library of the University of Tokyo Drug Discovery Initiative, the structure-activity relationship of the unique substrate-competitive inhibitors was established with the help of X-ray crystallography and fragment molecular orbital (FMO) calculations for the ligand-protein interaction. Further optimization of the in vitro characteristics and drug metabolism and pharmacokinetics (DMPK) properties led to the identification of 26j (RK-701), which is a structurally distinct potent inhibitor of G9a/GLP (IC ₅₀ = 27/53 nM). Compound 26j exhibited remarkable selectivity against other related methyltransferases, dose-dependent attenuation of cellular H3K9me2 levels, and tumor growth inhibition in MOLT-4 cells in vitro . Moreover, compound 26j showed inhibition of tumor initiation and growth in a carcinogen-induced hepatocellular carcinoma (HCC) in vivo mouse model without overt acute toxicity.

Organizational Affiliation

Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan.

Macromolecule Content

Total Structure Weight: 67.68 kDa
Atom Count: 5,120
Modeled Residue Count: 538
Deposited Residue Count: 566
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	283	Homo sapiens	Mutation(s): 0 Gene Names: EHMT2, BAT8, C6orf30, G9A, KMT1C, NG36 EC: 2.1.1 (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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I6Z (Subject of Investigation/LOI) Query on I6Z Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B]	I [auth A], P [auth B]	~{N}-[(2~{S})-4-cyclopropyl-1-oxidanylidene-1-phenylazanyl-butan-2-yl]-3,6,6-trimethyl-4-oxidanylidene-5,7-dihydro-1~{H}-indole-2-carboxamide C₂₅ H₃₁ N₃ O₃ FSDGOJSCOXFEFN-SFHVURJKSA-N		Interactions Focus chain I [auth A] Focus chain P [auth B] Interactions & Density Focus chain I [auth A] Focus chain P [auth B]
SFG Query on SFG Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain H [auth A]	H [auth A], O [auth B]	SINEFUNGIN C₁₅ H₂₃ N₇ O₅ LMXOHSDXUQEUSF-YECHIGJVSA-N		Interactions Focus chain H [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain O [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain L [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] K [auth B] C [auth A], D [auth A], E [auth A], F [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	J [auth A], R [auth B], S [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]