4Z4B | pdb_00004z4b

2-Pyridyl Hoechst - a New Generation DNA-Binding Radioprotector

• PDB DOI: https://doi.org/10.2210/pdb4Z4B/pdb
• NAKB: 4Z4B

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


• Deposited: 2015-04-01 Released: 2016-05-04 
• Deposition Author(s): Wee, J.-Y., Dobson, R.C.J., White, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.211 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: other

Literature

2-Pyridyl Hoechst - a New Generation DNA-Binding Radioprotector

Wee, J.-Y., Dobson, R.C.J., White, J.M.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.76 kDa 
• Atom Count: 616 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')	A, B	12	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4L1	C [auth A]	5-(4-methylpiperazin-1-yl)-2'-(pyridin-2-yl)-1H,1'H-2,5'-bibenzimidazole C24 H23 N7 QLJMJDOZNAQXQQ-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.211 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.858	α = 90
b = 40.797	β = 90
c = 64.538	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Wee, J.-Y., Dobson, R.C.J., White, J.M.

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2026-03-04
  Changes: Refinement description, Structure summary