9LNH | pdb_00009lnh

Crystal structure of Peroxiredoxin I in complex with compound LC-PDin20


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 
    0.202 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Rapid Discovery of Celastrol Derivatives as Potent and Selective PRDX1 Inhibitors via Microplate-Based Parallel Compound Library and In Situ Screening.

Chen, S.Wang, Z.Gao, J.Wang, Y.Liang, J.Zhu, Y.Xu, H.Chen, K.Jin, L.Zhang, H.Xiong, H.Luo, C.

(2025) J Med Chem 68: 13609-13627

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00433
  • Primary Citation of Related Structures:  
    9LNH

  • PubMed Abstract: 

    Celastrol has been identified as a reactive oxygen species (ROS) elevator that reduces cancer cell proliferation by inhibiting peroxiredoxin (PRDX) activity, albeit with poor selectivity. We describe a semiautomated and microplate-based parallel compound library approach leading to the rapid discovery of celastrol derivatives that are potent and selective PRDX1 inhibitors. Amide coupling and the urea bond forming reactions were used to construct a 2720-member celastrol derivative library, followed by in situ PRDX1 enzyme inhibition assay screening, leading to the rapid identification of a series of celastrol derivatives demonstrating promising PRDX1 inhibition activity. Compound LC-PDin06 displayed the best anti-PRDX1 activity (IC 50 = 0.042 μM) with selectivity toward the PRDX family, as well as good antiproliferative activity against colorectal cancer cells. A cocrystal structure of PRDX1 with LC-PDin20 and molecular docking studies provided insight into the binding mode of the inhibitors with PRDX1, aiding in the structure-based design of future PRDX1 inhibitors.


  • Organizational Affiliation
    • School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxiredoxin-1
A, B
175Homo sapiensMutation(s): 2 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EL9 (Subject of Investigation/LOI)
Query on A1EL9

Download Ideal Coordinates CCD File 
C [auth A](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]butanoic acid
C33 H46 N2 O5
PMMICXSXMUCBMJ-XSZYYSLISA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free:  0.202 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.391α = 90
b = 77.84β = 90
c = 82.136γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Database references