8X73 | pdb_00008x73

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


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
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted YC0Click on this verticalbar to view details

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Literature

Discovery of a Novel Orally Bioavailable FLT3-PROTAC Degrader for Efficient Treatment of Acute Myeloid Leukemia and Overcoming Resistance of FLT3 Inhibitors.

Wang, J.Rong, Q.Ye, L.Fang, B.Zhao, Y.Sun, Y.Zhou, H.Wang, D.He, J.Cui, Z.Zhang, Q.Kang, D.Hu, L.

(2024) J Med Chem 67: 7197-7223

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00051
  • Primary Citation of Related Structures:  
    8X71, 8X73

  • PubMed Abstract: 

    Fms-like tyrosine receptor kinase 3 (FLT3) proteolysis-targeting chimeras (PROTACs) represent a promising approach to eliminate the resistance of FLT3 inhibitors. However, due to the poor druggability of PROTACs, the development of orally bioavailable FLT3-PROTACs faces great challenges. Herein, a novel orally bioavailable FLT3-ITD degrader A20 with excellent pharmacokinetic properties was discovered through reasonable design. A20 selectively inhibited the proliferation of FLT3-ITD mutant acute myeloid leukemia (AML) cells and potently induced FLT3-ITD degradation through the ubiquitin-proteasome system. Notably, oral administration of A20 resulted in complete tumor regression on subcutaneous AML xenograft models. Furthermore, on systemic AML xenograft models, A20 could completely eliminate the CD45 + CD33 + human leukemic cells in murine and significantly prolonged the survival time of mice. Most importantly, A20 exerted significantly improved antiproliferative activity against drug-resistant AML cells compared to existing FLT3 inhibitors. These findings suggested that A20 could serve as a promising drug candidate for relapsed or refractory AML.


  • Organizational Affiliation

    Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, P. R. 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YC0 (Subject of Investigation/LOI)
Query on YC0

Download Ideal Coordinates CCD File 
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 = 64.307α = 90
b = 77.928β = 90
c = 81.339γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted YC0Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81903538

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release