5LV2

Crystal structure of mouse CARM1 in complex with inhibitor LH1246


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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, E, F, G, H
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 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LHB
Query on LHB

Download CCD File 
B, D, F, H
5-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]methyl]-4-azanyl-1-(methoxymethyl)pyrimidin-2-one
C17 H23 N9 O5
XNIWXZNBHJGVPA-UBEDBUPSSA-N
 Ligand Interaction
SAO
Query on SAO

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A, C, E, G
5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine
C14 H21 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-O
 Ligand Interaction
PG4
Query on PG4

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C, D, F
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
M2M
Query on M2M

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C, E
1-METHOXY-2-(2-METHOXYETHOXY)ETHANE
C6 H14 O3
SBZXBUIDTXKZTM-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
DXE
Query on DXE

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C
1,2-DIMETHOXYETHANE
C4 H10 O2
XTHFKEDIFFGKHM-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B, C, D, E, F, G, H
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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D, F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.684α = 90
b = 74.832β = 90.53
c = 206.639γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references