9HXV | pdb_00009hxv

Crystal structure of TET2-DNA in complex with IOX1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.221 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.191 (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

Advancing TET Inhibitor Development: From Structural Insights to Biological Evaluation.

Willems, S.Maksumic, L.Niggenaber, J.Lin, T.C.Schulz, T.Weisner, J.Sievers, S.Muller, M.P.Summerer, D.Rauh, D.

(2025) ACS Med Chem Lett 16: 804-810

  • DOI: https://doi.org/10.1021/acsmedchemlett.5c00042
  • Primary Citation of Related Structures:  
    9HXV

  • PubMed Abstract: 

    Ten-eleven translocation (TET) methylcytosine dioxygenases are part of the epigenetic regulatory machinery that erases DNA methylation. Aberrant TET activities are frequently found in hematopoietic malignancies, where loss of TET2 function leads to DNA hypermethylation. A comprehensive understanding of the biological role of TETs is essential to elucidate disease pathogenesis and identify novel therapeutic strategies. We present a robust pipeline integrating protein X-ray crystallography, molecular modeling, and pharmacophore analysis to advance the current TET inhibitor development. In addition, we have synthesized and evaluated a series of 8-hydroxyquinoline (8-HQ) derivatives, demonstrating their potential as chemical tools to explore TET function further. These findings lay the groundwork for a TET-centered therapeutic approach.


  • Organizational Affiliation
    • Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD) am Zentrum für integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Str. 4a, 44227 Dortmund, Germany.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methylcytosine dioxygenase TET2467Homo sapiensMutation(s): 0 
Gene Names: TET2KIAA1546Nbla00191
EC: 1.14.11.80
UniProt & NIH Common Fund Data Resources
Find proteins for Q6N021 (Homo sapiens)
Explore Q6N021 
Go to UniProtKB:  Q6N021
PHAROS:  Q6N021
GTEx:  ENSG00000168769 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6N021
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
12mer-DNA
B, C
12Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8XQ (Subject of Investigation/LOI)
Query on 8XQ

Download Ideal Coordinates CCD File 
H [auth A]8-hydroxyquinoline-5-carboxylic acid
C10 H7 N O3
JGRPKOGHYBAVMW-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
D [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.221 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.44α = 90
b = 89.13β = 90
c = 268.25γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermany01ZX2201B
European Regional Development FundEuropean UnionEFRE-800400
Other governmentNW21-062C
Other privateEx-2021-0033
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Database references