ISDA

Entry Detail

PDB ID:

5V3H

Keywords:

TRANSFERASE/TRANSFERASE inhibitor

Title:

Crystal structure of SMYD2 with SAM and EPZ033294

Biological Source:

Source Organism:

Homo sapiens

Host Organism:

Spodoptera frugiperda

PDB Version:

Deposition Date:

2017-03-07

Release Date:

2018-04-25

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.69 Å

R-Value Free:

0.27

R-Value Work:

0.21

R-Value Observed:

0.22

Space Group:

C 1 2 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:N-lysine methyltransferase SMYD2
Mutations:N-terminal His tag with TEV cleavage site and FLAG tag
Chain IDs:A
Chain Length:444
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NRG4 Pfam ID:PF00856, PF01753

Ligand Molecules

8WG

EDO

GOL

PEG

SAM

Primary Citation

Small molecule inhibitors and CRISPR/Cas9 mutagenesis demonstrate that SMYD2 and SMYD3 activity are dispensable for autonomous cancer cell proliferation.

Thomenius, M.J, Totman, J, Harvey, D, Mitchell, L.H, Riera, T.V, Cosmopoulos, K, Grassian, A.R, Klaus, C, Foley, M, Admirand, E.A, Jahic, H, Majer, C, Wigle, T, Jacques, S.L, Gureasko, J, Brach, D, Lingaraj, T, West, K, Smith, S, Rioux, N, Waters, N.J, Tang, C, Raimondi, A, Munchhof, M, Mills, J.E, Ribich, S, Porter Scott, M, Kuntz, K.W, Janzen, W.P, Moyer, M, Smith, J.J, Chesworth, R, Copeland, R.A, Boriack-Sjodin, P.A.Show

Plos One 13 e0197372 e0197372 (2018)

PMID: 29856759 DOI: 10.1371/journal.pone.0197372

Abstact

A key challenge in the development of precision medicine is defining the phenotypic consequences of pharmacological modulation of specific target macromolecules. To address this issue, a variety of genetic, molecular and chemical tools can be used. All of these approaches can produce misleading results if the specificity of the tools is not well understood and the proper controls are not performed. In this paper we illustrate these general themes by providing detailed studies of small molecule inhibitors of the enzymatic activity of two members of the SMYD branch of the protein lysine methyltransferases, SMYD2 and SMYD3. We show that tool compounds as well as CRISPR/Cas9 fail to reproduce many of the cell proliferation findings associated with SMYD2 and SMYD3 inhibition previously obtained with RNAi based approaches and with early stage chemical probes.

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Primary Citation of related structures