8X73 | pdb_00008x73

Crystal structure of Peroxiredoxin I in complex with compound 19-069

• PDB DOI: https://doi.org/10.2210/pdb8X73/pdb

• Classification: OXIDOREDUCTASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-11-22 Released: 2024-06-19 
• Deposition Author(s): Zhang, H., Luo, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Discovery of Urea Derivatives of Celastrol as Selective Peroxiredoxin 1 Inhibitors against Colorectal Cancer Cells

Li, Y., Zhu, Y., Shang, F.F., Xu, L., Jiang, D., Sun, B., Zhang, L., Luo, C., Zhang, A., Zhang, H., Ding, C.

(2024) J Med Chem 67: 7176-7196

• DOI: https://doi.org/10.1021/acs.jmedchem.4c00023

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 39.81 kDa 
• Atom Count: 3,292 
• Modeled Residue Count: 344 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxiredoxin-1	A, B	175	Homo sapiens	Mutation(s): 2  Gene Names: PRDX1, PAGA, PAGB, TDPX2 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YC0 (Subject of Investigation/LOI)	C [auth A], D [auth B]	methyl (2~{S})-2-[[(2~{R},4~{a}~{S},6~{a}~{R},6~{a}~{S},14~{a}~{S},14~{b}~{R})-2,4~{a},6~{a},6~{a},9,14~{a}-hexamethyl-10-oxidanyl-11-oxidanylidene-1,3,4,5,6,13,14,14~{b}-octahydropicen-2-yl]carbamoylamino]-3-oxidanyl-propanoate C33 H46 N2 O6 PJLZTFVARNCYGK-CPKSEDGTSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.307	α = 90
b = 77.928	β = 90
c = 81.339	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Zhang, H., Luo, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81903538

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release
  
• Version 1.1: 2025-12-03
  Changes: Database references, Structure summary