6P6G

Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of Isoxazole Amides as Potent and Selective SMYD3 Inhibitors.

Su, D.S.Qu, J.Schulz, M.Blackledge, C.W.Yu, H.Zeng, J.Burgess, J.Reif, A.Stern, M.Nagarajan, R.Pappalardi, M.B.Wong, K.Graves, A.P.Bonnette, W.Wang, L.Elkins, P.Knapp-Reed, B.Carson, J.D.McHugh, C.Mohammad, H.Kruger, R.Luengo, J.Heerding, D.A.Creasy, C.L.

(2020) ACS Med Chem Lett 11: 133-140

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00493
  • Primary Citation of Related Structures:  
    6P6G, 6P6K, 6P7Z, 6PAF

  • PubMed Abstract: 

    We report herein the discovery of isoxazole amides as potent and selective SET and MYND Domain-Containing Protein 3 (SMYD3) inhibitors. Elucidation of the structure-activity relationship of the high-throughput screening (HTS) lead compound 1 provided potent and selective SMYD3 inhibitors. The SAR optimization, cocrystal structures of small molecules with SMYD3, and mode of inhibition (MOI) characterization of compounds are described. The synthesis and biological and pharmacokinetic profiles of compounds are also presented.


  • Organizational Affiliation

    Medicinal Chemistry, Medicine Design, Oncology R&D, Data and Computational Sciences, and Protein Cellular and Structural Sciences, Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SMYD3432Homo sapiensMutation(s): 0 
Gene Names: SMYD3ZMYND1ZNFN3A1
EC: 2.1.1.43
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LUP (Subject of Investigation/LOI)
Query on LUP

Download Ideal Coordinates CCD File 
K [auth A]5-cyclopropyl-N-{1-[({trans-4-[(4,4,4-trifluorobutyl)amino]cyclohexyl}methyl)sulfonyl]piperidin-4-yl}-1,2-oxazole-3-carboxamide
C23 H35 F3 N4 O4 S
VAYJCVQRMIULEM-SAABIXHNSA-N
SAH
Query on SAH

Download Ideal Coordinates CCD File 
J [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-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
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
LUP BindingDB:  6P6G Ki: 6 (nM) from 1 assay(s)
IC50: min: 3.2, max: 67 (nM) from 2 assay(s)
EC50: 39 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.433α = 90
b = 66.636β = 90
c = 107.34γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references, Derived calculations