7LZF

Crystal Structure of SETD2 bound to Compound 57


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of a First-in-Class Inhibitor of the Histone Methyltransferase SETD2 Suitable for Preclinical Studies.

Lampe, J.W.Alford, J.S.Boriak-Sjodin, P.A.Brach, D.Cosmopoulos, K.Duncan, K.W.Eckley, S.T.Foley, M.A.Harvey, D.M.Motwani, V.Munchhof, M.J.Raimondi, A.Riera, T.V.Tang, C.Thomenius, M.J.Totman, J.Farrow, N.A.

(2021) ACS Med Chem Lett 12: 1539-1545

  • DOI: 10.1021/acsmedchemlett.1c00272
  • Primary Citation of Related Structures:  
    7LZB, 7LZD, 7LZF

  • PubMed Abstract: 
  • SET domain-containing protein 2 (SETD2), a histone methyltransferase, has been identified as a target of interest in certain hematological malignancies, including multiple myeloma. This account details the discovery of EPZ-719 , a novel and potent SETD2 inhibitor with a high selectivity over other histone methyltransferases ...

    SET domain-containing protein 2 (SETD2), a histone methyltransferase, has been identified as a target of interest in certain hematological malignancies, including multiple myeloma. This account details the discovery of EPZ-719 , a novel and potent SETD2 inhibitor with a high selectivity over other histone methyltransferases. A screening campaign of the Epizyme proprietary histone methyltransferase-biased library identified potential leads based on a 2-amidoindole core. Structure-based drug design (SBDD) and drug metabolism/pharmacokinetics (DMPK) optimization resulted in EPZ-719 , an attractive tool compound for the interrogation of SETD2 biology that enables in vivo target validation studies.


    Organizational Affiliation

    Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SETD2A278Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYW2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YHV (Subject of Investigation/LOI)
Query on YHV

Download Ideal Coordinates CCD File 
F [auth A]4-fluoro-N-[(1R,3S)-3-{(3S)-3-[(methanesulfonyl)(methyl)amino]pyrrolidin-1-yl}cyclohexyl]-7-methyl-1H-indole-2-carboxamide
C22 H31 F N4 O3 S
ZLVKIBLQXFILMA-IKGGRYGDSA-N
 Ligand Interaction
SAM
Query on SAM

Download Ideal Coordinates CCD File 
E [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.91α = 90
b = 76.648β = 90
c = 76.186γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata 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: 2021-09-22
    Type: Initial release
  • Version 1.1: 2021-11-03
    Changes: Database references