Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 32.97 kDa 
• Atom Count: 1993 
• Modelled Residue Count: 235 
• Deposited Residue Count: 278 
• Unique protein chains: 1

7LZB

Crystal Structure of SETD2 bound to Compound 2

• PDB DOI: 10.2210/pdb7LZB/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Baculovirus expression vector pFastBac1-HM
• Mutation(s): No 


• Deposited: 2021-03-09 Released: 2021-09-22 
• Deposition Author(s): Farrow, N.A., Boriack-Sjodin, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.264 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 

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

• PubMed: 34671445 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SETD2	A	278	Homo sapiens	Mutation(s): 0  Gene Names: SETD2, HIF1, HYPB, KIAA1732, KMT3A, SET2, HSPC069 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	E [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
YJ1 (Subject of Investigation/LOI)	F [auth A]	N-[(1r,4r)-4-(beta-alanylamino)cyclohexyl]-7-methyl-1H-indole-2-carboxamide C19 H26 N4 O2 AEUGFQSECICIPH-SHTZXODSSA-N
BME	G [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.264 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.545	α = 90
b = 76.751	β = 90
c = 77.775	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2021-03-09 
• Released Date: 2021-09-22 
Deposition Author(s): Farrow, N.A., Boriack-Sjodin, P.

Revision History  

• Version 1.0: 2021-09-22
  Type: Initial release
  
• Version 1.1: 2021-11-03
  Changes: Database references