9DEX | pdb_00009dex

Crystal structure of human peroxiredoxin 1 in complex with inhibitor WF-097


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.192 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Mechanism-based peroxiredoxin 3 inhibitors exploit a covalent warhead for cancer therapy.

Nelson, K.J.Smalley Jr., T.L.Messier, T.Gumpena, R.Gandhi, U.Milczarek, S.Habibovic, A.Hoffman, H.Gibson, V.Hondal, R.J.Lowther, W.T.Cunniff, B.

(2025) Sci Adv 11: eady4492-eady4492

  • DOI: https://doi.org/10.1126/sciadv.ady4492
  • Primary Citation of Related Structures:  
    9DEX

  • PubMed Abstract: 

    Covalent inhibitors that are approved and marketed drugs exploit a wide array of warheads and reactions with amino acid side chain-based nucleophiles. Thiostrepton (TS) inhibits the peroxidase activity of the mitochondrial antioxidant protein peroxiredoxin 3 by forming a covalent crosslink between the two active site cysteine residues. Peroxiredoxin 3 inactivation increases reactive oxygen species levels, induces cancer cell death in preclinical models, and shows promise in an ongoing clinical trial for malignant mesothelioma using direct pleural infusion. We report the identification of the minimal fragment of TS that contains tandem dehydro-alanine (DHA) moieties and maintains anticancer activity while losing interactions with three alternative targets of intact TS. Biochemical, kinetic, cellular, and structural studies demonstrate that this fragment is a mechanism-based peroxiredoxin inhibitor. These findings represent a promising start toward a pro-oxidant approach for cancer therapy. Moreover, the data support that the DHA moiety should be added to the covalent warhead arsenal.


  • Organizational Affiliation
    • Department of Biochemistry, Center for Structural Biology, Wake Forest University School of Medicine, Medical Center Blvd., Winston-Salem, NC 27157, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxiredoxin-1
A, B
198Homo sapiensMutation(s): 3 
Gene Names: PRDX1PAGAPAGBTDPX2
EC: 1.11.1.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q06830 (Homo sapiens)
Explore Q06830 
Go to UniProtKB:  Q06830
PHAROS:  Q06830
GTEx:  ENSG00000117450 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06830
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IY4 (Subject of Investigation/LOI)
Query on IY4

Download Ideal Coordinates CCD File 
Z [auth B]methyl N-(2-{[(2M)-2-(pyridin-3-yl)-1,3-thiazole-4-carbonyl]amino}prop-2-enoyl)-D-alaninate
C16 H16 N4 O4 S
RVPKOYWAKLWTTB-SNVBAGLBSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
L [auth A],
O [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A],
Q [auth B],
U [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
F [auth A]
H [auth A]
I [auth A]
C [auth A],
D [auth A],
F [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth A],
N [auth A],
P [auth A],
R [auth B],
S [auth B],
T [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.192 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.315α = 90
b = 78.799β = 90
c = 83.071γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

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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: 2025-10-29
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Database references