5V37 | pdb_00005v37

Crystal structure of SMYD3 with SAM and EPZ028862


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 
    0.279 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5V37

Ligand Structure Quality Assessment 


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: https://doi.org/10.1371/journal.pone.0197372
  • Primary Citation Related Structures: 
    5V37, 5V3H

  • 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. 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.

Macromolecule Content 

  • Total Structure Weight: 50.62 kDa 
  • Atom Count: 4,275 
  • Modeled Residue Count: 424 
  • Deposited Residue Count: 428 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SMYD3428Homo sapiensMutation(s): 0 
Gene Names: SMYD3ZMYND1ZNFN3A1
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7B4 (Homo sapiens)
Explore Q9H7B4 
Go to UniProtKB:  Q9H7B4
PHAROS:  Q9H7B4
GTEx:  ENSG00000185420 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H7B4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8WD

Query on 8WD



Download:Ideal Coordinates CCD File
F [auth A]N-{(3-endo)-8-[(trans-4-aminocyclohexyl)sulfonyl]-8-azabicyclo[3.2.1]octan-3-yl}-5-cyclopropyl-1,2-oxazole-3-carboxamide
C20 H30 N4 O4 S
JYZQPJRVTADXNE-BSBCAUIJSA-N
SAM

Query on SAM



Download:Ideal Coordinates CCD File
E [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
G [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
8WD BindingDB:  5V37 IC50: 1.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free:  0.279 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.818α = 90
b = 65.868β = 90
c = 107.015γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
KYLINdata reduction
KYLINdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references