9EYX

Human PRMT5 in complex with AZ compound 28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.270 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

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This is version 1.1 of the entry. See complete history


Literature

Discovery and In Vivo Efficacy of AZ-PRMT5i-1, a Novel PRMT5 Inhibitor with High MTA Cooperativity.

Smith, J.M.Barlaam, B.Beattie, D.Bradshaw, L.Chan, H.M.Chiarparin, E.Collingwood, O.Cooke, S.L.Cronin, A.Cumming, I.Dean, E.Debreczeni, J.E.Del Barco Barrantes, I.Diene, C.Gianni, D.Guerot, C.Guo, X.Guven, S.Hayhow, T.G.Hong, T.Kemmitt, P.D.Lamont, G.M.Lamont, S.Lynch, J.T.McWilliams, L.Moore, S.Raubo, P.Robb, G.R.Robinson, J.Scott, J.S.Srinivasan, B.Steward, O.Stubbs, C.J.Syson, K.Tan, L.Turner, O.Underwood, E.Urosevic, J.Vazquez-Chantada, M.Whittaker, A.L.Wilson, D.M.Winter-Holt, J.J.

(2024) J Med Chem 67: 13604-13638

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00097
  • Primary Citation of Related Structures:  
    9EYU, 9EYV, 9EYW, 9EYX

  • PubMed Abstract: 

    PRMT5, a type 2 arginine methyltransferase, has a critical role in regulating cell growth and survival in cancer. With the aim of developing MTA-cooperative PRMT5 inhibitors suitable for MTAP-deficient cancers, herein we report our efforts to develop novel "MTA-cooperative" compounds identified through a high-throughput biochemical screening approach. Optimization of hits was achieved through structure-based design with a focus on improvement of oral drug-like properties. Bioisosteric replacement of the original thiazole guanidine headgroup, spirocyclization of the isoindolinone amide scaffold to both configurationally and conformationally lock the bioactive form, and fine-tuning of the potency, MTA cooperativity, and DMPK properties through specific substitutions of the azaindole headgroup were conducted. We have identified an orally available in vivo lead compound, 28 ("AZ-PRMT5i-1"), which shows sub-10 nM PRMT5 cell potency, >50-fold MTA cooperativity, suitable DMPK properties for oral dosing, and significant PRMT5-driven in vivo efficacy in several MTAP-deficient preclinical cancer models.


  • Organizational Affiliation

    Research and Early Development, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 5, N-terminally processed637Homo sapiensMutation(s): 0 
Gene Names: PRMT5HRMT1L5IBP72JBP1SKB1
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 WDR77342Homo 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
A1H73 (Subject of Investigation/LOI)
Query on A1H73

Download Ideal Coordinates CCD File 
C [auth A](3~{S})-2-[(5-azanyl-6-fluoranyl-1~{H}-pyrrolo[3,2-b]pyridin-2-yl)methyl]-6-fluoranyl-1'-[(4-fluorophenyl)methyl]spiro[isoindole-3,3'-pyrrolidine]-1,2'-dione
C26 H20 F3 N5 O2
BJIUKEMXFQJDBZ-SANMLTNESA-N
MTA
Query on MTA

Download Ideal Coordinates CCD File 
D [auth A]5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.270 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.124α = 90
b = 139.123β = 90
c = 178.145γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Database references