9RDI | pdb_00009rdi

Crystal Structure of Flap Endonuclease FEN1 with Compound 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.232 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Fragment-Based Discovery and Structure-Led Optimization of MSC778, the First Potent, Selective, and Orally Bioavailable FEN1 Inhibitor.

Mann, S.E.Lefranc, J.Alkhatib, O.Boivin, R.Bomke, J.Byrne, R.T.Cassona, C.P.Chen, X.Cornaciu, I.Costales, P.Davis, O.A.DeSelm, L.Elinati, E.Follows, B.Galbiati, A.Goldner, C.Hayre, J.K.Jorand-Lebrun, C.Lademann, C.A.Leuthner, B.Majithiya, J.B.Malta, C.F.Mason, B.McWhirter, C.L.Neff, B.Nissink, J.W.M.Pehl, U.Petersson, C.Pica, A.Pinto, M.F.Rajendra, E.Rakers, C.Toste Rego, A.Robinson, H.M.R.Sala-Hojman, A.Schaedler, T.A.Schurmann, P.J.L.Silva, D.O.Smith, G.C.M.Sorrell, F.Webster, G.R.Zenke, F.T.Heald, R.A.Burgdorf, L.T.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01526
  • Primary Citation of Related Structures:  
    9RCI, 9RDI

  • PubMed Abstract: 

    Flap endonuclease 1 (FEN1) is a long-standing target of interest in the DNA damage response (DDR) field due to its therapeutic potential in BRCA mutant cancers. To-date there have only been a handful of FEN1 inhibitors reported in the literature, most of which display modest selectivity and/or weak cellular activity. As such, there is a need for more advanced pharmacological tools to probe the biology of FEN1. Here, we report the discovery of MSC778 , the first potent, selective, and orally bioavailable FEN1 inhibitor. We describe our metal-chelating fragment screening approach and structure-based optimization to identify MSC778 , using structural insights to drive design. Consistent with FEN1 inhibition, MSC778 selectively kills BRCA2 -deficient cells and potentiates the activity of PARPi niraparib in vivo to induce tumor stasis in a BRCA2 KO DLD-1 mouse xenograft. Furthermore, we illustrate how development of this approach has the potential for addressing nucleases as a target class.


  • Organizational Affiliation
    • Artios Pharma Ltd., B940, Babraham Research Campus, Cambridge CB22 3FH, U.K.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flap endonuclease 1
A, B
342Homo sapiensMutation(s): 0 
Gene Names: FEN1RAD2
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P39748 (Homo sapiens)
Explore P39748 
Go to UniProtKB:  P39748
PHAROS:  P39748
GTEx:  ENSG00000168496 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39748
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TEW
Query on TEW

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
K [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
6-tungstotellurate(VI)
O24 Te W6
JDLYBIMRCSJRQJ-UHFFFAOYSA-M
A1JED (Subject of Investigation/LOI)
Query on A1JED

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
2-methyl-9-oxidanyl-6-(phenylmethyl)-3,4-dihydropyrazino[1,2-c]pyrimidine-1,8-dione
C15 H15 N3 O3
RPOUCHBGKZYIOF-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
P [auth B],
Q [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.232 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.453α = 90
b = 116.15β = 90
c = 139.706γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited Kingdom--
Other privateGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release
  • Version 1.1: 2025-10-01
    Changes: Database references