1X26 | pdb_00001x26

Solution structure of the AA-mismatch DNA complexed with naphthyridine-azaquinolone

• PDB DOI: https://doi.org/10.2210/pdb1X26/pdb
• NAKB: 1X26

• Classification: DNA
• Mutation(s): No 


• Deposited: 2005-04-20 Released: 2006-04-04 
• Deposition Author(s): Nakatani, K., Hagihara, S., Goto, Y., Kobori, A., Hagihara, M., Hayashi, G., Kyo, M., Nomura, M., Mishima, M., Kojima, C.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 150 
• Conformers Submitted: 30 
• Selection Criteria: structures with the lowest energy 

Literature

Small-molecule ligand induces nucleotide flipping in (CAG)n trinucleotide repeats

Nakatani, K., Hagihara, S., Goto, Y., Kobori, A., Hagihara, M., Hayashi, G., Kyo, M., Nomura, M., Mishima, M., Kojima, C.

(2005) Nat Chem Biol 1: 39-43

• PubMed: 16407992 
• DOI: https://doi.org/10.1038/nchembio708
• Primary Citation Related Structures: 
  1X26


• PubMed Abstract: 
  

  DNA trinucleotide repeats, particularly CXG, are common within the human genome. However, expansion of trinucleotide repeats is associated with a number of disorders, including Huntington disease, spinobulbar muscular atrophy and spinocerebellar ataxia. In these cases, the repeat length is known to correlate with decreased age of onset and disease severity. Repeat expansion of (CAG)n, (CTG)n and (CGG)n trinucleotides may be related to the increased stability of alternative DNA hairpin structures consisting of CXG-CXG triads with X-X mismatches. Small-molecule ligands that selectively bound to CAG repeats could provide an important probe for determining repeat length and an important tool for investigating the in vivo repeat extension mechanism. Here we report that napthyridine-azaquinolone (NA, 1) is a ligand for CAG repeats and can be used as a diagnostic tool for determining repeat length. We show by NMR spectroscopy that binding of NA to CAG repeats induces the extrusion of a cytidine nucleotide from the DNA helix.

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Organizational Affiliation: 
• Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.63 kDa 
• Atom Count: 514 
• Modeled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*TP*AP*AP*CP*AP*GP*AP*AP*TP*G)-3'	A	11	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*AP*TP*TP*CP*AP*GP*TP*TP*AP*G)-3'	B	11	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAZ	C [auth A], D [auth B]	N~3~-{3-[(7-METHYL-1,8-NAPHTHYRIDIN-2-YL)AMINO]-3-OXOPROPYL}-N~1~-[(7-OXO-7,8-DIHYDRO-1,8-NAPHTHYRIDIN-2-YL)METHYL]-BET A-ALANINAMIDE C24 H25 N7 O3 BWINWCKASXYPFA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 150 
• Conformers Submitted: 30 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-04 
Deposition Author(s): Nakatani, K., Hagihara, S., Goto, Y., Kobori, A., Hagihara, M., Hayashi, G., Kyo, M., Nomura, M., Mishima, M., Kojima, C.

Revision History  

• Version 1.0: 2006-04-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-02
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2024-05-29
  Changes: Data collection