6P6K

Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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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: 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 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SMYD3A432Homo sapiensMutation(s): 0 
Gene Names: SMYD3, ZMYND1, ZNFN3A1
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM
Download Ideal Coordinates CCD File 
H [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N		 Ligand Interaction
L0J (Subject of Investigation/LOI)
Query on L0J
Download Ideal Coordinates CCD File 
I [auth A]N-{1-[(2-aminoethyl)sulfonyl]piperidin-4-yl}-5-cyclopropyl-1,2-oxazole-3-carboxamide
C14 H22 N4 O4 S
AMCHZZBLDUVCGF-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
G [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.719α = 90
b = 66.038β = 90
c = 105.773γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2019-06-04 
  • Released Date: 2020-01-15 
    • Deposition Author(s): Elkins, P.A., Wang, L.

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