6D2L | pdb_00006d2l

Crystal structure of human CARM1 with (S)-SKI-72


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.236 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6D2L

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 237.96 kDa 
  • Atom Count: 16,868 
  • Modeled Residue Count: 1,976 
  • Deposited Residue Count: 2,064 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone-arginine methyltransferase CARM1
A, B, C, D, E
A, B, C, D, E, F
344Homo sapiensMutation(s): 0 
Gene Names: CARM1PRMT4
EC: 2.1.1.319
UniProt & NIH Common Fund Data Resources
Find proteins for Q86X55 (Homo sapiens)
Explore Q86X55 
Go to UniProtKB:  Q86X55
PHAROS:  Q86X55
GTEx:  ENSG00000142453 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86X55
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FTG

Query on FTG



Download:Ideal Coordinates CCD File
G [auth A]
L [auth B]
M [auth C]
P [auth D]
Q [auth E]
G [auth A],
L [auth B],
M [auth C],
P [auth D],
Q [auth E],
R [auth F]
(2S,5S)-2-amino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-5-[(benzylamino)methyl]-N-[2-(4-hydroxyphenyl)ethyl]hexanamide
C31 H40 N8 O5
BSSHHGWCSNARRG-FRWVVBMCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
H [auth A],
N [auth C],
S [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
UNX

Query on UNX



Download:Ideal Coordinates CCD File
K [auth A],
O [auth C],
T [auth F]
UNKNOWN ATOM OR ION
X

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.236 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.601α = 90
b = 155.638β = 101.04
c = 95.338γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2023-08-16
    Changes: Data collection, Database references