8Q60 | pdb_00008q60

Experimental Data Snapshot

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

(2025) Angew Chem Int Ed Engl 64: e202505273-e202505273

PubMed Abstract:
A linker unit was designed and synthesized that can serve both as a hairpin turn in a DNA duplex and anchor point for an aromatic helical foldamer mimicking the shape and surface properties of B-DNA. Methods were developed to synthesize natural/non-natural chimeric molecules combining foldamer and DNA segments. The ability of the linker to position the foldamer helix and the duplex DNA so that their rims and grooves are in register, despite their completely different chemical nature, was demonstrated using single crystal X-ray diffraction, circular dichroism and molecular models. Bio-layer interferometry confirmed that artificial hairpin DNA duplexes keep their ability to bind to DNA binding proteins. The chimeric molecules may pave the way to competitive inhibitors of protein-DNA interactions involving sequence-selective DNA-binding proteins.

Organizational Affiliation

Macromolecule Content

Macromolecules

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Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(GPTPTPTPTPG)-3'	A, B [auth D]	6	synthetic construct
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(CPAPAPAPAP*C)-3')	C [auth B], D [auth E]	6	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JY9 (Subject of Investigation/LOI) Query on JY9 Download Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain E [auth A] MOL2 format, chain G [auth D] MOL2 format, chain E [auth A] mmCIF format, chain G [auth D] mmCIF format, chain E [auth A]	E [auth A], G [auth D]	4-[8-(aminomethyl)-2-[[5-(3-oxidanylpropyl)quinolin-8-yl]carbamoyl]quinolin-4-yl]butyl dihydrogen phosphite C₂₇ H₃₁ N₄ O₅ P BOKZCLFXARXCEP-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth E] SDF format, chain F [auth D] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth E] MOL2 format, chain F [auth D] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth E] mmCIF format, chain F [auth D]	F [auth D], H [auth B], I [auth B], J [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth D] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth E] Interactions & Density Focus chain F [auth D] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth E]