4Y30

Crystal structure of human protein arginine methyltransferase PRMT6 bound to SAH and EPZ020411


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: 10.1021/acsmedchemlett.5b00071
  • Structures With Same Primary Citation

  • 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 ha ...

    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.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein arginine N-methyltransferase 6
A, B
351Homo sapiensMutation(s): 0 
Gene Names: PRMT6HRMT1L6
EC: 2.1.1 (PDB Primary Data), 2.1.1.125 (PDB Primary Data), 2.1.1.319 (UniProt)
Find proteins for Q96LA8 (Homo sapiens)
Go to UniProtKB:  Q96LA8
NIH Common Fund Data Resources
PHAROS  Q96LA8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
49L
Query on 49L

Download CCD File 
A, B
N,N'-dimethyl-N-({3-[4-({trans-3-[2-(tetrahydro-2H-pyran-4-yl)ethoxy]cyclobutyl}oxy)phenyl]-1H-pyrazol-4-yl}methyl)ethane-1,2-diamine
C25 H38 N4 O3
QMDKVNSQXPVCRD-RQNOJGIXSA-N
 Ligand Interaction
SAH
Query on SAH

Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
49LIC50:  10   nM  Binding MOAD
49LIC50:  10   nM  BindingDB
49LIC50:  637   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.672α = 90
b = 99.672β = 90
c = 89.252γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2015-07-08
    Changes: Database references