5V3H

Crystal structure of SMYD2 with SAM and EPZ033294


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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.

(2018) PLoS One 13: e0197372-e0197372

  • DOI: 10.1371/journal.pone.0197372
  • Primary Citation of Related Structures:  
    5V3H, 5V37

  • PubMed Abstract: 
  • 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. A ...

    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.


    Organizational Affiliation

    Epizyme, Inc., Cambridge, Massachusetts, United States of America.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-lysine methyltransferase SMYD2A444Homo sapiensMutation(s): 0 
Gene Names: SMYD2KMT3C
EC: 2.1.1 (PDB Primary Data), 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
Find proteins for Q9NRG4 (Homo sapiens)
Explore Q9NRG4 
Go to UniProtKB:  Q9NRG4
NIH Common Fund Data Resources
PHAROS  Q9NRG4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8WG
Query on 8WG

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A
N-[1-({1-[(4-chlorophenyl)methyl]-1H-pyrazol-4-yl}methyl)azetidin-3-yl]-1-cyclopropyl-1H-1,2,3-triazole-4-carboxamide
C20 H22 Cl N7 O
MOWCUCXGYVJUHU-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

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A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.56α = 90
b = 54.775β = 114.22
c = 79.702γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2017-03-07 
  • Released Date: 2018-04-25 
  • Deposition Author(s): Boriack-Sjodin, P.A.

Revision History 

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-06-13
    Changes: Data collection, Structure summary
  • Version 1.2: 2019-05-08
    Changes: Data collection, Database references