7TY2 | pdb_00007ty2

Crystal Structure of SETD2 Bound to an Indole-based Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 
    0.270 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted KS6Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Conformational-Design-Driven Discovery of EZM0414: A Selective, Potent SETD2 Inhibitor for Clinical Studies.

Alford, J.S.Lampe, J.W.Brach, D.Chesworth, R.Cosmopoulos, K.Duncan, K.W.Eckley, S.T.Kutok, J.L.Raimondi, A.Riera, T.V.Shook, B.Tang, C.Totman, J.Farrow, N.A.

(2022) ACS Med Chem Lett 13: 1137-1143

  • DOI: https://doi.org/10.1021/acsmedchemlett.2c00167
  • Primary Citation of Related Structures:  
    7TY2, 7TY3

  • PubMed Abstract: 

    SETD2, a lysine N -methyltransferase, is a histone methyltransferase that plays an important role in various cellular processes and was identified as a target of interest in multiple myeloma that features a t(4,14) translocation. We recently reported the discovery of a novel small-molecule SETD2 inhibitor tool compound that is suitable for preclinical studies. Herein we describe the conformational-design-driven evolution of the advanced chemistry lead, which resulted in compounds appropriate for clinical evaluation. Further optimization of this chemical series led to the discovery of EZM0414, which is a potent, selective, and orally bioavailable inhibitor of SETD2 with good pharmacokinetic properties and robust pharmacodynamic activity in a mouse xenograft model.


  • Organizational Affiliation

    Epizyme Inc., 50 Hampshire Street, Sixth Floor, Cambridge, Massachusetts 02139, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SETD2278Homo sapiensMutation(s): 0 
Gene Names: SETD2HIF1HYPBKIAA1732KMT3ASET2HSPC069
EC: 2.1.1.359 (PDB Primary Data), 2.1.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYW2 (Homo sapiens)
Explore Q9BYW2 
Go to UniProtKB:  Q9BYW2
PHAROS:  Q9BYW2
GTEx:  ENSG00000181555 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYW2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
KS6 BindingDB:  7TY2 IC50: min: 18, max: 31 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free:  0.270 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.693α = 90
b = 75.74β = 90
c = 75.923γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted KS6Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data

  • Released Date: 2022-08-31 
  • Deposition Author(s): Farrow, N.A.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-31
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Data collection
  • Version 1.2: 2024-04-03
    Changes: Refinement description