9VA3 | pdb_00009va3

Solution NMR structures of hTERT DNA G-quadruplexes (G4s) in complex with small molecule ZBH-01

  • Classification: DNA
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2025-06-02 Released: 2026-02-11 
  • Deposition Author(s): Zeng, L.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 9VA3

This is version 1.2 of the entry. See complete history

Literature

Dual targeting of topoisomerase I and DNA G-quadruplexes enhances senescence and chemosensitivity in colorectal cancer.

Li, Y.Ji, D.Jia, Y.Liang, Y.Wei, E.Gao, C.Li, Y.Zeng, C.Wang, L.Wang, C.Guo, Z.Zhang, Y.Zhou, M.M.Wu, D.Zeng, L.

(2026) Commun Biol 9

  • DOI: https://doi.org/10.1038/s42003-026-09801-w
  • Primary Citation Related Structures: 
    9VA0, 9VA3

  • PubMed Abstract: 

    Colorectal cancer (CRC) remains a therapeutic challenge due to chemoresistance that limits conventional treatment efficacy. We developed ZBH-01, a camptothecin derivative engineered to target both topoisomerase I (TOP1) and DNA G-quadruplexes (G4s). Unlike irinotecan (CPT-11), which requires metabolic activation, ZBH-01 directly stabilizes TOP1-DNA covalent complexes and preferentially binds the hTERT promoter G4, a regulator of telomere maintenance and oncogenic transcription. Structural studies reveal that the crescent-shaped scaffold of ZBH-01 π-π stacks onto the external G-tetrad of the hTERT G4, displacing SP1/MYC transcription factors and suppressing hTERT expression. Functionally, ZBH-01 demonstrated improved efficacy in chemoresistant models, exhibiting 14-fold and 7-fold greater efficacy than CPT-11 and SN-38 respectively in cisplatin-resistant cells, and outperforming CPT-11 by 61-fold and SN-38 by 2.4-fold in 5-FU-resistant models. By concurrently disrupting DNA repair through TOP1-trapping and transcriptional adaptation via G4-stabilization, ZBH-01 induced DNA damage, telomere shortening, and cellular senescence. These findings establish TOP1/G4 dual-targeting as a potential therapeutic strategy to enhance CRC chemosensitivity, presenting a new framework for combining DNA damage induction with transcription modulation.


  • Organizational Affiliation
    • Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China.

Macromolecule Content 

  • Total Structure Weight: 7.59 kDa 
  • Atom Count: 506 
  • Modeled Residue Count: 22 
  • Deposited Residue Count: 22 
  • Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*AP*TP*GP*GP*GP*AP*GP*GP*GP*TP*CP*TP*GP*GP*GP*AP*GP*GP*GP*CP*C)-3')22Homo sapiens
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EQ9
(Subject of Investigation/LOI)

Query on A1EQ9



Download:Ideal Coordinates CCD File
D [auth A](S)-4,11-diethyl-4-hydroxy-3,14-dioxo-3,4,12,14-tetrahydro-1H-pyrano[3',4':6,7]indolizino[1,2-b]quinolin-9-yl (2-(4-methylpiperazin-1-yl)-2-oxoethyl)carbamate
C30 H33 N5 O7
VULZRDFNTXNECE-PMERELPUSA-N
K

Query on K



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2026-02-11 
  • Deposition Author(s): Zeng, L.

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

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-11
    Type: Initial release
  • Version 1.1: 2026-04-01
    Changes: Database references
  • Version 1.2: 2026-05-06
    Changes: Database references