4Y2H

Crystal structure of human protein arginine methyltransferase PRMT6 bound to SAH and an aryl pyrazole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4Y2H/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-02-09 Released: 2015-04-22 
• Deposition Author(s): Swinger, K.K., Boriack-Sjodin, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 0.232 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Aryl Pyrazoles as Potent Inhibitors of Arginine Methyltransferases: Identification of the First PRMT6 Tool Compound.

Mitchell, L.H., Drew, A.E., Ribich, S.A., Rioux, N., Swinger, K.K., Jacques, S.L., Lingaraj, T., Boriack-Sjodin, P.A., Waters, N.J., Wigle, T.J., Moradei, O., Jin, L., Riera, T., Porter-Scott, M., Moyer, M.P., Smith, J.J., Chesworth, R., Copeland, R.A.

(2015) ACS Med Chem Lett 6: 655-659

• PubMed: 26101569 
• DOI: https://doi.org/10.1021/acsmedchemlett.5b00071
• Primary Citation of Related Structures:  
  4Y2H, 4Y30


• PubMed Abstract: 
  

  A novel aryl pyrazole series of arginine methyltransferase inhibitors has been identified. Synthesis of analogues within this series yielded the first potent, selective, small molecule PRMT6 inhibitor tool compound, EPZ020411. PRMT6 overexpression has been reported in several cancer types suggesting that inhibition of PRMT6 activity may have therapeutic utility. Identification of EPZ020411 provides the field with the first small molecule tool compound for target validation studies. EPZ020411 shows good bioavailability following subcutaneous dosing in rats making it a suitable tool for in vivo studies.

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Organizational Affiliation: 

Epizyme, Inc. , 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02138, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 80.61 kDa 
• Atom Count: 5,822 
• Modelled Residue Count: 689 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 6	A, B	352	Homo sapiens	Mutation(s): 0  Gene Names: PRMT6, HRMT1L6 EC: 2.1.1 (PDB Primary Data), 2.1.1.125 (PDB Primary Data), 2.1.1.319 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LA8 (Homo sapiens) Explore Q96LA8  Go to UniProtKB:  Q96LA8
PHAROS:  Q96LA8 GTEx:  ENSG00000198890

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A], E [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
49K	D [auth A], F [auth B]	N-{[5-(4-fluorophenyl)-1H-pyrazol-4-yl]methyl}-N-methylethane-1,2-diamine C13 H17 F N4 WJJPSVIYQWOSFK-UHFFFAOYSA-N
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
49K	BindingDB:  4Y2H	IC50: 11 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 0.232 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.97	α = 90
b = 99.97	β = 90
c = 89.49	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-22 
Deposition Author(s): Swinger, K.K., Boriack-Sjodin, P.A.

Revision History  

• Version 1.0: 2015-04-22
  Type: Initial release
  
• Version 1.1: 2015-07-08
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references