9HXV | pdb_00009hxv

Crystal structure of TET2-DNA in complex with IOX1

PDB DOI: https://doi.org/10.2210/pdb9HXV/pdb
NAKB: 9HXV

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-01-08 Released: 2025-04-09
Deposition Author(s): Niggenaber, J., Mueller, M.P., Rauh, D.
Funding Organization(s): German Federal Ministry for Education and Research, European Regional Development Fund, Other government, Other private, German Research Foundation (DFG)

Experimental Data Snapshot

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

Starting Model: experimental
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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

PubMed: 40365382 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.5c00042
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 59.79 kDa
Atom Count: 3,885
Modeled Residue Count: 428
Deposited Residue Count: 491
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylcytosine dioxygenase TET2	A	467	Homo sapiens	Mutation(s): 0 Gene Names: TET2, KIAA1546, Nbla00191 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6N021
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
12mer-DNA	B, C	12	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8XQ (Subject of Investigation/LOI) Query on 8XQ Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	8-hydroxyquinoline-5-carboxylic acid C₁₀ H₇ N O₃ JGRPKOGHYBAVMW-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

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

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.44	α = 90
b = 89.13	β = 90
c = 268.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	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: 2025-04-09

Deposition Author(s):

Niggenaber, J.

Mueller, M.P.

Rauh, D.

Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	01ZX2201B
European Regional Development Fund	European Union	EFRE-800400
Other government		NW21-062C
Other private		Ex-2021-0033
German Research Foundation (DFG)	Germany	--