9CJW | pdb_00009cjw

The 24mer DNA Duplex 5'-GCTGGAAAGTTTAAACTTTCCAGC-3' Bound by the Diamidine DB2447 at Single G Sites

PDB DOI: https://doi.org/10.2210/pdb9CJW/pdb
NAKB: 9CJW

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

Deposited: 2024-07-08 Released: 2025-08-06
Deposition Author(s): Terrell, J.R., Ogbonna, E.N., Paul, A., Wilson, W.D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.267 (Depositor), 0.266 (DCC)
R-Value Work:
0.220 (Depositor), 0.223 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Sequence Recognition in the Minor Groove: Single G Targeting by Diamidine Small Molecules

Terrell, J.R., Ogbonna, E.N., Paul, A., Poon, G.M.K., Wilson, W.D.

To be published.

Macromolecule Content

Total Structure Weight: 16.16 kDa
Atom Count: 1,210
Modeled Residue Count: 48
Deposited Residue Count: 48
Unique nucleic acid chains: 3

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(GPCPTPGPGPAPAPAPGPTPTPT)-3')	A	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(GPCPTPGPGPAPAPAPGPTPTPTPAPAPAPCPTPTPTPCPCPAPGPC)-3')	B [auth C]	24	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PAPAPAPCPTPTPTPCPCPAPGPC)-3')	C [auth B]	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AAQ (Subject of Investigation/LOI) Query on A1AAQ Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain D [auth A] MOL2 format, chain K [auth C] MOL2 format, chain D [auth A] mmCIF format, chain K [auth C] mmCIF format, chain D [auth A]	D [auth A], K [auth C]	4,4'-[pyridine-2,6-diylbis(methyleneoxy)]di(benzene-1-carboximidamide) C₂₁ H₂₁ N₅ O₂ UDMQJIVHWQYKTJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth C]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [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] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth C], M [auth C], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]