ISDA: 4YND

Deposition Date 2015-03-09

Release Date 2015-05-20

Last Version Date 2023-09-27

Entry Detail

PDB ID:

4YND

Keywords:

Transferase/Inhibitor

Title:

The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Spodoptera frugiperda

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.79 Å

R-Value Free:

0.25

R-Value Work:

0.19

R-Value Observed:

0.20

Space Group:

P 21 21 21

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:N-lysine methyltransferase SMYD2
Gene (Uniprot):SMYD2
Chain IDs:A
Chain Length:461
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NRG4 Pfam ID:PF01753, PF00856

Ligand Molecules

4GQ

SAM

Primary Citation

Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2.

Sweis, R.F, Wang, Z, Algire, M, Arrowsmith, C.H, Brown, P.J, Chiang, G.G, Guo, J, Jakob, C.G, Kennedy, S, Li, F, Maag, D, Shaw, B, Soni, N.B, Vedadi, M, Pappano, W.N.Show

Acs Med.Chem.Lett. 6 695 700 (2015)

PMID: 26101576 DOI: 10.1021/acsmedchemlett.5b00124

Abstact

A lack of useful small molecule tools has precluded thorough interrogation of the biological function of SMYD2, a lysine methyltransferase with known tumor-suppressor substrates. Systematic exploration of the structure-activity relationships of a previously known benzoxazinone compound led to the synthesis of A-893, a potent and selective SMYD2 inhibitor (IC50: 2.8 nM). A cocrystal structure reveals the origin of enhanced potency, and effective suppression of p53K370 methylation is observed in a lung carcinoma (A549) cell line.

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Primary Citation of related structures