Crystal structure of SmyD3 in complex with covalent inhibitor 4

Experimental Data Snapshot

  • Resolution: 2.13 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Discovery of Irreversible Inhibitors Targeting Histone Methyltransferase, SMYD3.

Huang, C.Liew, S.S.Lin, G.R.Poulsen, A.Ang, M.J.Y.Chia, B.C.S.Chew, S.Y.Kwek, Z.P.Wee, J.L.K.Ong, E.H.Retna, P.Baburajendran, N.Li, R.Yu, W.Koh-Stenta, X.Ngo, A.Manesh, S.Fulwood, J.Ke, Z.Chung, H.H.Sepramaniam, S.Chew, X.H.Dinie, N.Lee, M.A.Chew, Y.S.Low, C.B.Pendharkar, V.Manoharan, V.Vuddagiri, S.Sangthongpitag, K.Joy, J.Matter, A.Hill, J.Keller, T.H.Foo, K.

(2019) ACS Med Chem Lett 10: 978-984

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00170
  • Primary Citation of Related Structures:  
    5YJO, 6IJL

  • PubMed Abstract: 

    SMYD3 is a histone methyltransferase that regulates gene transcription, and its overexpression is associated with multiple human cancers. A novel class of tetrahydroacridine compounds which inhibit SMYD3 through a covalent mechanism of action is identified. Optimization of these irreversible inhibitors resulted in the discovery of 4-chloroquinolines, a new class of covalent warheads. Tool compound 29 exhibits high potency by inhibiting SMYD3's enzymatic activity and showing antiproliferative activity against HepG2 in 3D cell culture. Our findings suggest that covalent inhibition of SMYD3 may have an impact on SMYD3 biology by affecting expression levels, and this warrants further exploration.

  • Organizational Affiliation

    Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SMYD3423Homo sapiensMutation(s): 2 
EC: (PDB Primary Data), (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7B4 (Homo sapiens)
Explore Q9H7B4 
Go to UniProtKB:  Q9H7B4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H7B4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.13 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.428α = 90
b = 66.181β = 90
c = 107.648γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Advisory, Data collection, Database references, Derived calculations