ISDA

Deposition Date 2024-04-20

Release Date 2025-01-22

Last Version Date 2025-01-22

Entry Detail

PDB ID:

8Z7E

Keywords:

TRANSFERASE

Title:

Structure of G9a in complex with compound 9b

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.55 Å

R-Value Free:

0.19

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

P 1 21 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone-lysine N-methyltransferase EHMT2
Gene (Uniprot):EHMT2
Chain IDs:A, B
Chain Length:283
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q96KQ7 Pfam ID:PF05033, PF00856 EC:2.1.1.355

Ligand Molecules

A1L09

SFG

Primary Citation

Structure-based development of novel substrate-type G9a inhibitors as epigenetic modulators for sickle cell disease treatment.

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

Bioorg.Med.Chem.Lett. 110 129856 129856 (2024)

PMID: 38914346 DOI: 10.1016/j.bmcl.2024.129856

Abstact

The discovery and development of structurally distinct lysine methyltransferase G9a inhibitors have been the subject of intense research in epigenetics. Structure-based optimization was conducted, starting with the previously reported seed compound 7a and lead to the identification of a highly potent G9a inhibitor, compound 7i (IC50 = 0.024 μM). X-ray crystallography for the ligand-protein interaction and kinetics study, along with surface plasmon resonance (SPR) analysis, revealed that compound 7i interacts with G9a in a unique binding mode. In addition, compound 7i caused attenuation of cellular H3K9me2 levels and induction of γ-globin mRNA expression in HUDEP-2 cells in a dose-dependent manner.

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Protein

Chemical

Disease

Primary Citation of related structures