21HS | pdb_000021hs

Crystal structure of d(CGTTAACG)2 in complex with N-[3-[4-[3-(acridin-9-ylamino)propyl]piperazin-1-yl]propyl]acridin-9-amine

PDB DOI: https://doi.org/10.2210/pdb21HS/pdb
Entry: 21HS supersedes: 9MBW

Classification: DNA
Organism(s): DNA molecule
Mutation(s): No

Deposited: 2025-12-12 Released: 2026-05-27
Deposition Author(s): Lee, H.C., Hou, M.H.
Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.256 (Depositor), 0.256 (DCC)
R-Value Work:
0.204 (Depositor), 0.206 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of d(CGTTAACG)2 in complex with N-[3-[4-[3-(acridin-9-ylamino)propyl]piperazin-1-yl]propyl]acridin-9-amine

Lee, H.C., Hou, M.H.

To be published.

Macromolecule Content

Total Structure Weight: 5.41 kDa
Atom Count: 397
Modeled Residue Count: 16
Deposited Residue Count: 16
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA (5'-D(CPGPTPTPAPAPCPG)-3')	A, B	8	DNA molecule
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L8R (Subject of Investigation/LOI) Query on A1L8R Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	N-[3-[4-[3-(acridin-9-ylamino)propyl]piperazin-1-yl]propyl]acridin-9-amine C₃₆ H₃₈ N₆ AAMSBOZZFRTUFD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.256 (Depositor), 0.256 (DCC)
R-Value Work: 0.204 (Depositor), 0.206 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 23.681	α = 90
b = 41.286	β = 90
c = 43.294	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-27

Deposition Author(s):

This entry supersedes: 9MBW

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	113-2311-B- 005-006-MY3
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	113-2113-M-005-016-MY3

Revision History (Full details and data files)

Version 1.0: 2026-05-27
Type: Initial release

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