9C10 | pdb_00009c10

AMG 193, a clinical stage MTA-cooperative PRMT5 inhibitor, drives anti-tumor activity preclinically and in patients with MTAP-deleted cancers


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.299 (Depositor), 0.288 (DCC) 
  • R-Value Work: 
    0.261 (Depositor), 0.258 (DCC) 
  • R-Value Observed: 
    0.263 (Depositor) 

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

AMG 193, a Clinical Stage MTA-Cooperative PRMT5 Inhibitor, Drives Antitumor Activity Preclinically and in Patients with MTAP-Deleted Cancers.

Belmontes, B.Slemmons, K.K.Su, C.Liu, S.Policheni, A.N.Moriguchi, J.Tan, H.Xie, F.Aiello, D.A.Yang, Y.Lazaro, R.Aeffner, F.Rees, M.G.Ronan, M.M.Roth, J.A.Vestergaard, M.Cowland, S.Andersson, J.Sarvary, I.Chen, Q.Sharma, P.Lopez, P.Tamayo, N.Pettus, L.H.Ghimire-Rijal, S.Mukund, S.Allen, J.R.DeVoss, J.Coxon, A.Rodon, J.Ghiringhelli, F.Penel, N.Prenen, H.Glad, S.Chuang, C.H.Keyvanjah, K.Townsley, D.M.Butler, J.R.Bourbeau, M.P.Caenepeel, S.Hughes, P.E.

(2025) Cancer Discov 15: 139-161

  • DOI: https://doi.org/10.1158/2159-8290.CD-24-0887
  • Primary Citation of Related Structures:  
    9C10

  • PubMed Abstract: 

    One of the most robust synthetic lethal interactions observed in multiple functional genomic screens has been dependency on PRMT5 in cancer cells with MTAP deletion. We report the discovery of the clinical stage MTA-cooperative PRMT5 inhibitor AMG 193, which preferentially binds PRMT5 in the presence of MTA and has potent biochemical and cellular activity in MTAP-deleted cells across multiple cancer lineages. In vitro, PRMT5 inhibition induces DNA damage, cell cycle arrest, and aberrant alternative mRNA splicing in MTAP-deleted cells. In human cell line and patient-derived xenograft models, AMG 193 induces robust antitumor activity and is well tolerated with no impact on normal hematopoietic cell lineages. AMG 193 synergizes with chemotherapies or the KRAS G12C inhibitor sotorasib in vitro, and combination treatment in vivo significantly inhibits tumor growth. AMG 193 is demonstrating promising clinical activity, including confirmed partial responses in patients with MTAP-deleted solid tumors from an ongoing phase 1/2 study.


  • Organizational Affiliation

    Amgen Inc., Thousand Oaks, CA, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 5650Homo 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 50344Homo 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ATH (Subject of Investigation/LOI)
Query on A1ATH

Download Ideal Coordinates CCD File 
F [auth A](4-amino-1,3-dihydrofuro[3,4-c][1,7]naphthyridin-8-yl){(3S)-3-[4-(trifluoromethyl)phenyl]morpholin-4-yl}methanone
C22 H19 F3 N4 O3
BFEBTMFPRJPBTK-LJQANCHMSA-N
MTA
Query on MTA

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

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.299 (Depositor), 0.288 (DCC) 
  • R-Value Work:  0.261 (Depositor), 0.258 (DCC) 
  • R-Value Observed: 0.263 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.653α = 90
b = 138.157β = 90
c = 178.336γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata 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: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Database references, Structure summary
  • Version 1.2: 2024-11-27
    Changes: Refinement description
  • Version 1.3: 2025-01-22
    Changes: Database references