6UXY

PRMT5:MEP50 Complexed with Allosteric Inhibitor Compound 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

Allosteric Modulation of Protein Arginine Methyltransferase 5 (PRMT5).

Palte, R.L.Schneider, S.E.Altman, M.D.Hayes, R.P.Kawamura, S.Lacey, B.M.Mansueto, M.S.Reutershan, M.Siliphaivanh, P.Sondey, C.Xu, H.Xu, Z.Ye, Y.Machacek, M.R.

(2020) ACS Med Chem Lett 11: 1688-1693

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00525
  • Primary Citation of Related Structures:  
    6UXX, 6UXY

  • PubMed Abstract: 

    Protein arginine methyltransferase 5 (PRMT5) belongs to a family of enzymes that regulate the posttranslational modification of histones and other proteins via methylation of arginine. Methylation of histones is linked to an increase in transcription and regulates a manifold of functions such as signal transduction and transcriptional regulation. PRMT5 has been shown to be upregulated in the tumor environment of several cancer types, and the inhibition of PRMT5 activity was identified as a potential way to reduce tumor growth. Previously, four different modes of PRMT5 inhibition were known-competing (covalently or non-covalently) with the essential cofactor S-adenosyl methionine (SAM), blocking the substrate binding pocket, or blocking both simultaneously. Herein we describe an unprecedented conformation of PRMT5 in which the formation of an allosteric binding pocket abrogates the enzyme's canonical binding site and present the discovery of potent small molecule allosteric PRMT5 inhibitors.


  • Organizational Affiliation

    Computational and Structural Chemistry, Discovery Chemistry, and Quantitative Biosciences, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 5645Homo sapiensMutation(s): 0 
Gene Names: PRMT5HRMT1L5IBP72JBP1SKB1
EC: 2.1.1.320
UniProt & NIH Common Fund Data Resources
Find proteins for O14744 (Homo sapiens)
Explore O14744 
Go to UniProtKB:  O14744
PHAROS:  O14744
GTEx:  ENSG00000100462 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14744
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Methylosome protein 50350Homo sapiensMutation(s): 0 
Gene Names: WDR77MEP50WD45HKMT1069Nbla10071
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQA1 (Homo sapiens)
Explore Q9BQA1 
Go to UniProtKB:  Q9BQA1
PHAROS:  Q9BQA1
GTEx:  ENSG00000116455 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BQA1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QKY (Subject of Investigation/LOI)
Query on QKY

Download Ideal Coordinates CCD File 
C [auth A](5R)-2-amino-5-(2-cyclohexylethyl)-3-methyl-5-phenyl-3,5-dihydro-4H-imidazol-4-one
C18 H25 N3 O
MVFBZVZUDDWALG-GOSISDBHSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.37α = 90
b = 140.8β = 90
c = 178.42γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description