9M3M | pdb_00009m3m

Structure of FSP1 in complex with FSEN1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.247 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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Literature

Cocrystal structure reveals the mechanism of FSP1 inhibition by FSEN1.

Zhang, S.Megarioti, A.H.Hendricks, J.M.Zhou, J.Sun, Q.Jia, D.Olzmann, J.A.

(2025) Proc Natl Acad Sci U S A 122: e2505197122-e2505197122

  • DOI: https://doi.org/10.1073/pnas.2505197122
  • Primary Citation of Related Structures:  
    9M3M

  • PubMed Abstract: 

    FSP1 is an FAD-dependent oxidoreductase that uses NAD(P)H to regenerate the reduced forms of lipophilic quinone antioxidants, such as coenzyme Q10 and vitamin K. These quinone antioxidants function as radical scavenging agents that prevent the propagation of lipid peroxidation and the induction of ferroptosis. Although several small-molecule inhibitors of FSP1 have been developed and found to sensitize cancer cells to ferroptosis, our understanding of their molecular mechanisms remains limited and no structures of FSP1 in complex with its inhibitors have been solved. Here, we solve the cocrystal structure of FSP1 in complex with the FSP1 inhibitor FSEN1, revealing that FSEN1 binds within the FSP1 substrate-binding pocket. FSEN1 makes key interactions with a critical phenylalanine, which is absent in mouse FSP1, providing an explanation for the selectivity of FSEN1 for human FSP1. These conclusions are supported by mutagenesis of FSP1 and biochemical and cellular assays of FSP1 function. Our findings provide the first cocrystal structure of FSP1 in complex with an inhibitor, enhancing our understanding of the mechanism of FSP1 inhibition and enabling future rational medicinal chemistry efforts to advance FSP1 inhibitors as therapeutics.


  • Organizational Affiliation
    • Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan 610041, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferroptosis suppressor protein 1A [auth C]373Homo sapiensMutation(s): 0 
Gene Names: AIFM2AMIDPRG3
EC: 1.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRQ8 (Homo sapiens)
Explore Q9BRQ8 
Go to UniProtKB:  Q9BRQ8
PHAROS:  Q9BRQ8
GTEx:  ENSG00000042286 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BRQ8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6FA
Query on 6FA

Download Ideal Coordinates CCD File 
C
6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O16 P2
BJSUUWFQAMLNKU-OKXKTURISA-N
NAP
Query on NAP

Download Ideal Coordinates CCD File 
B [auth C]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
A1EMU (Subject of Investigation/LOI)
Query on A1EMU

Download Ideal Coordinates CCD File 
D [auth C]3-(4-bromophenyl)-6-[[4-(4-methoxyphenyl)piperazin-1-yl]methyl]-[1,3]thiazolo[2,3-c][1,2,4]triazole
C22 H22 Br N5 O S
JGXIXBKKDUNARN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.247 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.539α = 90
b = 38.946β = 107.893
c = 70.097γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Cootmodel building
PHENIXphasing
ADDREFdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release