2Y1W

CRYSTAL STRUCTURE OF COACTIVATOR ASSOCIATED ARGININE METHYLTRANSFERASE 1 (CARM1) IN COMPLEX WITH SINEFUNGIN AND INDOLE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for Carm1 Inhibition by Indole and Pyrazole Inhibitors

Sack, J.S.Thieffine, S.Bandiera, T.Fasolini, M.Duke, G.J.Jayaraman, L.Kish, K.F.Klei, H.E.Purandare, A.V.Rosettani, P.Troiani, S.Xie, D.Bertrand, J.A.

(2011) Biochem.J. 436: 331

  • DOI: 10.1042/BJ20102161
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CARM1 (co-activator-associated arginine methyltransferase 1) is a PRMT (protein arginine N-methyltransferase) family member that catalyses the transfer of methyl groups from SAM (S-adenosylmethionine) to the side chain of specific arginine residues o ...

    CARM1 (co-activator-associated arginine methyltransferase 1) is a PRMT (protein arginine N-methyltransferase) family member that catalyses the transfer of methyl groups from SAM (S-adenosylmethionine) to the side chain of specific arginine residues of substrate proteins. This post-translational modification of proteins regulates a variety of transcriptional events and other cellular processes. Moreover, CARM1 is a potential oncological target due to its multiple roles in transcription activation by nuclear hormone receptors and other transcription factors such as p53. Here, we present crystal structures of the CARM1 catalytic domain in complex with cofactors [SAH (S-adenosyl-L-homocysteine) or SNF (sinefungin)] and indole or pyazole inhibitors. Analysis of the structures reveals that the inhibitors bind in the arginine-binding cavity and the surrounding pocket that exists at the interface between the N- and C-terminal domains. In addition, we show using ITC (isothermal titration calorimetry) that the inhibitors bind to the CARM1 catalytic domain only in the presence of the cofactor SAH. Furthermore, sequence differences for select residues that interact with the inhibitors may be responsible for the CARM1 selectivity against PRMT1 and PRMT3. Together, the structural and biophysical information should aid in the design of both potent and specific inhibitors of CARM1.


    Organizational Affiliation

    Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, NJ 08543-4000, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HISTONE-ARGININE METHYLTRANSFERASE CARM1
A, B, C, D
348Homo sapiensMutation(s): 0 
Gene Names: CARM1 (PRMT4)
EC: 2.1.1.319
Find proteins for Q86X55 (Homo sapiens)
Go to Gene View: CARM1
Go to UniProtKB:  Q86X55
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SFG
Query on SFG

Download SDF File 
Download CCD File 
A, B, C, D
SINEFUNGIN
ADENOSYL-ORNITHINE
C15 H23 N7 O5
LMXOHSDXUQEUSF-YECHIGJVSA-N
 Ligand Interaction
849
Query on 849

Download SDF File 
Download CCD File 
A, B, C, D
2-{4-[3-FLUORO-2-(2-METHOXYPHENYL)-1H-INDOL-5-YL] PIPERIDIN-1-YL}-N-METHYLETHANAMINE
C23 H28 F N3 O
SPSRJAZORUFUOI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
849Kd: 465 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 74.896α = 90.00
b = 98.471β = 90.00
c = 207.184γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
MOLREPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-23
    Type: Initial release
  • Version 1.1: 2011-05-19
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance