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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free:
0.187 (Depositor), 0.189 (DCC)
R-Value Work:
0.155 (Depositor), 0.156 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06830
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YC0 (Subject of Investigation/LOI) Query on YC0 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
YC0	BindingDB: 8X73	IC50: 470 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.187 (Depositor), 0.189 (DCC)
R-Value Work: 0.155 (Depositor), 0.156 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-06-19

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.