9DEX: Human peroxiredoxin 1

Crystal structure of human peroxiredoxin 1 in complex with inhibitor WF-097. Determined by X-ray diffraction at 2.3 Å resolution. Released 29 Oct 2025.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,943
Mol. weight: 45.93 kDa
Ligands: IY4
Released: 29 Oct 2025

Explore 9DEX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DEX contains 16 α-helices and 22 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	1
α-helix	12-14	3
β-strand	16-20	5	2
β-strand	26-30	5	2
α-helix	31-34	4
β-strand	38-43	6	2
α-helix	54-61	8
α-helix	63-67	5
β-strand	71-77	7	2
α-helix	81-88	8
α-helix	92-94	3
β-strand	104-106	3	2
α-helix	111-115	5
β-strand	119-120	2	3
β-strand	125-126	2	3
β-strand	128-133	6	2
β-strand	138	1	1
β-strand	139-145	7	2
α-helix	153-168	16

Chain B: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	4
α-helix	12-14	3
β-strand	16-20	5	2
β-strand	26-30	5	2
α-helix	31-34	4
β-strand	38-43	6	2
α-helix	54-61	8
α-helix	63-67	5
β-strand	71-77	7	2
α-helix	81-89	9
α-helix	92-94	3
β-strand	104-106	3	2
α-helix	111-116	6
β-strand	119-120	2	5
β-strand	125-126	2	5
β-strand	128-133	6	2
β-strand	138	1	4
β-strand	139-145	7	2
α-helix	153-167	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peroxiredoxin-1	A, B	protein	198	Homo sapiens	Q06830 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9DEX_1 Peroxiredoxin-1 (chains A, B)
SSGNAKIGHPAPNFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSD
RAEEFKKLNSQVIGASVDSHFSHLAWVNTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKA
DEGISFRGLFIIDDKGILRQITVNDLPVGRSVDETLRLVQAFQFTDKHGEVSPAGWKPGS
DTIKPDVQKSKEYFSKQK

Ligands and cofactors

ID	Name	Formula	Copies
IY4	methyl N-(2-{[(2M)-2-(pyridin-3-yl)-1,3-thiazole-4-carbonyl]amino}prop-2-enoyl)…	C16 H16 N4 O4 S	1

Water and common crystallization additives (PEG, SO4, EDO) are not listed.

Primary citation

Mechanism-based peroxiredoxin 3 inhibitors exploit a covalent warhead for cancer therapy. Nelson, K.J., Smalley Jr., T.L., Messier, T. et al. Sci Adv (2025) 11:eady4492-eady4492. DOI 10.1126/sciadv.ady4492 · PubMed

Other PDB entries of the same protein (UniProt Q06830 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8Z54 1.45 Å, Crystal structure of human SIRT5 in complex with succinylated Prx1 fragment
9VQ5 1.5 Å, Crystal structure of Peroxiredoxin I in complex with SAC
8X71 1.58 Å, Crystal structure of Peroxiredoxin I in complex with compound 19-064
8X73 1.61 Å, Crystal structure of Peroxiredoxin I in complex with compound 19-069
9LNH 1.63 Å, Crystal structure of Peroxiredoxin I in complex with compound LC-PDin20
9B7A 1.71 Å, Crystal structure of peroxiredoxin 1 with RA
7WET 1.76 Å, Crystal structure of Peroxiredoxin I in complex with the inhibitor Cela
9VGT 1.79 Å, Crystal structure of Peroxiredoxin I in complex with compound 19-150
9VE2 1.8 Å, Crystal Structure of Human Peroxiredoxin I in Complex with Fluvastatin
8Z56 1.81 Å, Crystal structure of human Q140L-SIRT5 in complex with succinylated Prx1 fragment
7WEU 1.81 Å, Crystal structure of Peroxiredoxin I in complex with compound 19-048
9LG0 1.81 Å, Crystal Structure of Human Peroxiredoxin I in Complex with SAB

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