Crystal structure of coactivator-associated arginine methyltransferase 1 with methylenesinefungin

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history


A chemical probe of CARM1 alters epigenetic plasticity against breast cancer cell invasion.

Cai, X.C.Zhang, T.Kim, E.J.Jiang, M.Wang, K.Wang, J.Chen, S.Zhang, N.Wu, H.Li, F.Dela Sena, C.C.Zeng, H.Vivcharuk, V.Niu, X.Zheng, W.Lee, J.P.Chen, Y.Barsyte, D.Szewczyk, M.Hajian, T.Ibanez, G.Dong, A.Dombrovski, L.Zhang, Z.Deng, H.Min, J.Arrowsmith, C.H.Mazutis, L.Shi, L.Vedadi, M.Brown, P.J.Xiang, J.Qin, L.X.Xu, W.Luo, M.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.47110
  • Primary Citation of Related Structures:  
    4IKP, 6D2L

  • PubMed Abstract: 

    CARM1 is a cancer-relevant protein arginine methyltransferase that regulates many aspects of transcription. Its pharmacological inhibition is a promising anti-cancer strategy. Here SKI-73 ( 6a in this work) is presented as a CARM1 chemical probe with pro-drug properties. SKI-73 ( 6a ) can rapidly penetrate cell membranes and then be processed into active inhibitors, which are retained intracellularly with 10-fold enrichment for several days. These compounds were characterized for their potency, selectivity, modes of action , and on-target engagement. SKI-73 ( 6a ) recapitulates the effect of CARM1 knockout against breast cancer cell invasion. Single-cell RNA-seq analysis revealed that the SKI-73 ( 6a )-associated reduction of invasiveness acts by altering epigenetic plasticity and suppressing the invasion-prone subpopulation. Interestingly, SKI-73 ( 6a ) and CARM1 knockout alter the epigenetic plasticity with remarkable difference, suggesting distinct modes of action for small-molecule and genetic perturbations. We therefore discovered a CARM1-addiction mechanism of cancer metastasis and developed a chemical probe to target this process.

  • Organizational Affiliation

    Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-arginine methyltransferase CARM1
A, B, C, D
341Homo sapiensMutation(s): 0 
Gene Names: CARM1PRMT4
EC: 2.1.1 (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q86X55 (Homo sapiens)
Explore Q86X55 
Go to UniProtKB:  Q86X55
GTEx:  ENSG00000142453 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86X55
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 4IK

Download Ideal Coordinates CCD File 
E [auth A],
GA [auth C],
Q [auth B],
TA [auth D]
(2S,5S)-2,6-diamino-5-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}hexanoic acid
C16 H25 N7 O5
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
HA [auth C],
IA [auth C],
JA [auth C],
UA [auth D]
C3 H8 O3
Query on UNX

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth D]
BA [auth B]
CA [auth B]
DA [auth B]
AA [auth B],
AB [auth D],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
M [auth A],
MA [auth C],
N [auth A],
NA [auth C],
O [auth A],
OA [auth C],
P [auth A],
PA [auth C],
QA [auth C],
R [auth B],
RA [auth C],
S [auth B],
SA [auth C],
T [auth B],
U [auth B],
V [auth B],
VA [auth D],
W [auth B],
WA [auth D],
X [auth B],
XA [auth D],
Y [auth B],
YA [auth D],
Z [auth B],
ZA [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.06α = 90
b = 98.844β = 90
c = 206.628γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-05-15
    Changes: Structure summary
  • Version 1.2: 2018-01-24
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2018-04-18
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2023-09-20
    Changes: Refinement description