6CKC

Structure of PRMT5:MEP50 in complex with LLY-283, a potent and selective inhibitor of PRMT5, with antitumor activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

LLY-283, a Potent and Selective Inhibitor of Arginine Methyltransferase 5, PRMT5, with Antitumor Activity.

Bonday, Z.Q.Cortez, G.S.Grogan, M.J.Antonysamy, S.Weichert, K.Bocchinfuso, W.P.Li, F.Kennedy, S.Li, B.Mader, M.M.Arrowsmith, C.H.Brown, P.J.Eram, M.S.Szewczyk, M.M.Barsyte-Lovejoy, D.Vedadi, M.Guccione, E.Campbell, R.M.

(2018) ACS Med Chem Lett 9: 612-617

  • DOI: 10.1021/acsmedchemlett.8b00014
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Protein arginine methyltransferase 5 (PRMT5) is a type II arginine methyltransferase that catalyzes the formation of symmetric dimethylarginine in a number of nuclear and cytoplasmic proteins. Although the cellular functions of PRMT5 have not been fu ...

    Protein arginine methyltransferase 5 (PRMT5) is a type II arginine methyltransferase that catalyzes the formation of symmetric dimethylarginine in a number of nuclear and cytoplasmic proteins. Although the cellular functions of PRMT5 have not been fully unraveled, it has been implicated in a number of cellular processes like RNA processing, signal transduction, and transcriptional regulation. PRMT5 is ubiquitously expressed in most tissues and its expression has been shown to be elevated in several cancers including breast cancer, gastric cancer, glioblastoma, and lymphoma. Here, we describe the identification and characterization of a novel and selective PRMT5 inhibitor with potent in vitro and in vivo activity. Compound 1 (also called LLY-283) inhibited PRMT5 enzymatic activity in vitro and in cells with IC 50 of 22 ± 3 and 25 ± 1 nM, respectively, while its diastereomer, compound 2 (also called LLY-284), was much less active. Compound 1 also showed antitumor activity in mouse xenografts when dosed orally and can serve as an excellent probe molecule for understanding the biological function of PRMT5 in normal and cancer cells.


    Organizational Affiliation

    Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein arginine N-methyltransferase 5
A
650Homo sapiensMutation(s): 0 
Gene Names: PRMT5HRMT1L5IBP72JBP1SKB1
EC: 2.1.1.320
Find proteins for O14744 (Homo sapiens)
Go to UniProtKB:  O14744
NIH Common Fund Data Resources
PHAROS  O14744

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Methylosome protein 50
B
344Homo sapiensMutation(s): 0 
Gene Names: WDR77MEP50WD45HKMT1069Nbla10071
Find proteins for Q9BQA1 (Homo sapiens)
Go to UniProtKB:  Q9BQA1
NIH Common Fund Data Resources
PHAROS  Q9BQA1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F5J
Query on F5J

Download CCD File 
A
7-[(5R)-5-C-phenyl-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine
C17 H18 N4 O4
WWOOWAHTEXIWBO-QFRSUPTLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.785α = 90
b = 139.077β = 90
c = 178.961γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-02-27 
  • Released Date: 2018-05-16 
  • Deposition Author(s): Antonysamy, S.

Revision History 

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