9V89 | pdb_00009v89

Crystal structure of d(CGTTAACG)2 with a five-carbon linker containing quinoxaline-acridine asymmetric intercalator compound

• PDB DOI: https://doi.org/10.2210/pdb9V89/pdb
• NAKB: 9V89

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2025-05-29 Released: 2026-06-03 
• Deposition Author(s): Wang, S.C., Hou, M.H.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 
  0.230 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Structural basis for asymmetric bis-intercalator targeting of DNA triplex junctions enabling dual inhibition of topoisomerase I and oncogene transcription.

Wang, S.C., Hsieh, C.C., Yuan, T.C., Lin, S.M., Chen, C.W., Chang, C.C., Huang, S.C., Wang, E.C., Huang, Y.J., Chiang, M.H., Horng, Y.C., Hou, M.H.

(2026) Nucleic Acids Res 54

• PubMed: 42206361 
• DOI: https://doi.org/10.1093/nar/gkag520
• Primary Citation Related Structures: 
  9V87, 9V88, 9V89


• PubMed Abstract: 
  

  Achieving multi-pathway suppression with minimal toxicity remains a major goal in anticancer drug design. Here, we present the structural and mechanistic basis for asymmetric bis-intercalators QA4 and QA5, which integrate weak (quinoxaline) and strong (acridine) chromophores through optimized alkyl linkers to achieve preference recognition of non-canonical DNA triplex junctions. High-resolution crystal structures reveal a spermine-stabilized triplex junction comprising minor-groove-mediated C:G-G triplets and sheared G-G interactions, distinct from classical Hoogsteen triplexes. QA compounds engage this topology via CpG step bis-intercalation, disrupting junction integrity and inducing localized DNA deformation. QA4, with a four-carbon linker, provides optimal spacing for dual chromophore engagement, producing pronounced helical distortion. Structure-function analyses indicate that acridine-mediated DNA distortion preferentially suppresses topoisomerase I, whereas quinoxaline-induced groove deformation is correlated with transcriptional repression of multiple oncogenes, including CEACAM6. In colorectal and lung cancer xenograft models, QA4 demonstrates potent antitumor activity with negligible hepatotoxicity. These findings define the structural principles underlying topology-driven DNA recognition and establish DNA triplex junctions as druggable targets for dual-function anticancer therapeutics.

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Organizational Affiliation: 
• Doctoral Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan.
Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan.
Institute of Chemistry, Academia Sinica, Taipei 11528, Taiwan.
Department of Chemistry, National Changhua University of Education, Changhua 50058, Taiwan.
Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan.
Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 5.52 kDa 
• Atom Count: 451 
• Modeled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*TP*TP*AP*AP*CP*G)-3')	A, B	8	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W1H (Subject of Investigation/LOI)	E [auth B]	N-[5-(acridin-9-ylamino)pentyl]quinoxaline-2-carboxamide C27 H25 N5 O FBSJAYALQSBKDK-UHFFFAOYSA-N
MPD	F [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CO	C [auth A], D [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free:  0.230 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 23.835	α = 90
b = 34.948	β = 90
c = 47.901	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-03 
Deposition Author(s): Wang, S.C., Hou, M.H.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	109-2628-M-005-001-MY4
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	109-2311-B-005-007-MY3

Revision History  

• Version 1.0: 2026-06-03
  Type: Initial release
  
• Version 1.1: 2026-06-10
  Changes: Database references