7SES

PRMT5/MEP50 with compound 29 bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Fragment-Based Discovery of MRTX1719, a Synthetic Lethal Inhibitor of the PRMT5•MTA Complex for the Treatment of MTAP -Deleted Cancers.

Smith, C.R.Aranda, R.Bobinski, T.P.Briere, D.M.Burns, A.C.Christensen, J.G.Clarine, J.Engstrom, L.D.Gunn, R.J.Ivetac, A.Jean-Baptiste, R.Ketcham, J.M.Kobayashi, M.Kuehler, J.Kulyk, S.Lawson, J.D.Moya, K.Olson, P.Rahbaek, L.Thomas, N.C.Wang, X.Waters, L.M.Marx, M.A.

(2022) J Med Chem 65: 1749-1766

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01900
  • Primary Citation of Related Structures:  
    7S0U, 7S1P, 7S1Q, 7S1R, 7S1S, 7SER, 7SES

  • PubMed Abstract: 

    The PRMT5•MTA complex has recently emerged as a new synthetically lethal drug target for the treatment of MTAP -deleted cancers. Here, we report the discovery of development candidate MRTX1719 . MRTX1719 is a potent and selective binder to the PRMT5•MTA complex and selectively inhibits PRMT5 activity in MTAP -deleted cells compared to MTAP -wild-type cells. Daily oral administration of MRTX1719 to tumor xenograft-bearing mice demonstrated dose-dependent inhibition of PRMT5-dependent symmetric dimethylarginine protein modification in MTAP -deleted tumors that correlated with antitumor activity. A 4-(aminomethyl)phthalazin-1(2 H )-one hit was identified through a fragment-based screen, followed by X-ray crystallography, to confirm binding to the PRMT5•MTA complex. Fragment growth supported by structural insights from X-ray crystallography coupled with optimization of pharmacokinetic properties aided the discovery of development candidate MRTX1719 .


  • Organizational Affiliation

    Mirati Therapeutics, San Diego, California 92121, 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
97X (Subject of Investigation/LOI)
Query on 97X

Download Ideal Coordinates CCD File 
C [auth A](2P)-2-{4-[4-(aminomethyl)-1-oxo-1,2-dihydrophthalazin-6-yl]-1-methyl-1H-pyrazol-5-yl}naphthalene-1-carbonitrile
C24 H18 N6 O
KRKVZAJFLCDWPU-UHFFFAOYSA-N
MTA (Subject of Investigation/LOI)
Query on MTA

Download Ideal Coordinates CCD File 
D [auth A]5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
MTA BindingDB:  7SES Kd: 661 (nM) from 1 assay(s)
97X BindingDB:  7SES IC50: min: 11, max: 1210 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.783α = 90
b = 138.053β = 90
c = 179.034γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-26
    Type: Initial release
  • Version 1.1: 2022-02-02
    Changes: Database references
  • Version 1.2: 2022-02-23
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description