5TBJ

Crystal structure of mouse CARM1 in complex with inhibitor LH1452


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation 3D Report Full Report



Literature

Hijacking DNA methyltransferase transition state analogues to produce chemical scaffolds for PRMT inhibitors.

Halby, L.Marechal, N.Pechalrieu, D.Cura, V.Franchini, D.M.Faux, C.Alby, F.Troffer-Charlier, N.Kudithipudi, S.Jeltsch, A.Aouadi, W.Decroly, E.Guillemot, J.C.Page, P.Ferroud, C.Bonnefond, L.Guianvarc'h, D.Cavarelli, J.Arimondo, P.B.

(2018) Philos Trans R Soc Lond B Biol Sci 373

  • DOI: 10.1098/rstb.2017.0072
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • DNA, RNA and histone methylation is implicated in various human diseases such as cancer or viral infections, playing a major role in cell process regulation, especially in modulation of gene expression. Here we developed a convergent synthetic pathwa ...

    DNA, RNA and histone methylation is implicated in various human diseases such as cancer or viral infections, playing a major role in cell process regulation, especially in modulation of gene expression. Here we developed a convergent synthetic pathway starting from a protected bromomethylcytosine derivative to synthesize transition state analogues of the DNA methyltransferases. This approach led to seven 5-methylcytosine-adenosine compounds that were, surprisingly, inactive against hDNMT1, hDNMT3Acat, TRDMT1 and other RNA human and viral methyltransferases. Interestingly, compound 4 and its derivative 2 showed an inhibitory activity against PRMT4 in the micromolar range. Crystal structures showed that compound 4 binds to the PRMT4 active site, displacing strongly the S -adenosyl-l-methionine cofactor, occupying its binding site, and interacting with the arginine substrate site through the cytosine moiety that probes the space filled by a substrate peptide methylation intermediate. Furthermore, the binding of the compounds induces important structural switches. These findings open new routes for the conception of new potent PRMT4 inhibitors based on the 5-methylcytosine-adenosine scaffold.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.


    Organizational Affiliation

    Churchill College, CB3 0DS Cambridge, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-arginine methyltransferase CARM1
A, B, C, D
361Mus musculusMutation(s): 0 
Gene Names: Carm1Prmt4
EC: 2.1.1.319
Find proteins for Q9WVG6 (Mus musculus)
Go to UniProtKB:  Q9WVG6
NIH Common Fund Data Resources
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LHD
Query on LHD

Download CCD File 
A, B, C, D
2-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]ethyl-[[4-azanyl-1-(methoxymethyl)-2-oxidanylidene-pyrimidin-5-yl]methyl]azanium
C18 H26 N9 O5
YHTQXGJBVFZAQM-CNEMSGBDSA-O
 Ligand Interaction
PG6
Query on PG6

Download CCD File 
B
1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
A, B, C
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
DXE
Query on DXE

Download CCD File 
A
1,2-DIMETHOXYETHANE
C4 H10 O2
XTHFKEDIFFGKHM-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.844α = 90
b = 99.2β = 90
c = 207.26γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 2.0: 2019-04-03
    Changes: Atomic model, Data collection, Database references