5LIT | pdb_00005lit

Structure of the DNA duplex d(AAATTT)2 with the potential antiparasitic drug 6XV at 1.25 A resolution

• PDB DOI: https://doi.org/10.2210/pdb5LIT/pdb
• NAKB: 5LIT

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


• Deposited: 2016-07-15 Released: 2017-06-14 
• Deposition Author(s): Millan, C.R., Dardonville, C., de Koning, H.P., Saperas, N., Lourdes Campos, J.
• Funding Organization(s): Government of Catalonia

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.121 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.123 (Depositor) 

Starting Model: other

Literature

Functional and structural analysis of AT-specific minor groove binders that disrupt DNA-protein interactions and cause disintegration of the Trypanosoma brucei kinetoplast.

Millan, C.R., Acosta-Reyes, F.J., Lagartera, L., Ebiloma, G.U., Lemgruber, L., Nue Martinez, J.J., Saperas, N., Dardonville, C., de Koning, H.P., Campos, J.L.

(2017) Nucleic Acids Res 45: 8378-8391

• PubMed: 28637278 
• DOI: https://doi.org/10.1093/nar/gkx521
• Primary Citation of Related Structures:  
  5LIT, 6GIM


• PubMed Abstract: 
  

  Trypanosoma brucei, the causative agent of sleeping sickness (Human African Trypanosomiasis, HAT), contains a kinetoplast with the mitochondrial DNA (kDNA), comprising of >70% AT base pairs. This has prompted studies of drugs interacting with AT-rich DNA, such as the N-phenylbenzamide bis(2-aminoimidazoline) derivatives 1 [4-((4,5-dihydro-1H-imidazol-2-yl)amino)-N-(4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)benzamide dihydrochloride] and 2 [N-(3-chloro-4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)-4-((4,5-dihydro-1H-imidazol-2-yl)amino)benzamide] as potential drugs for HAT. Both compounds show in vitro effects against T. brucei and in vivo curative activity in a mouse model of HAT. The main objective was to identify their cellular target inside the parasite. We were able to demonstrate that the compounds have a clear effect on the S-phase of T. brucei cell cycle by inflicting specific damage on the kinetoplast. Surface plasmon resonance (SPR)-biosensor experiments show that the drug can displace HMG box-containing proteins essential for kDNA function from their kDNA binding sites. The crystal structure of the complex of the oligonucleotide d[AAATTT]2 with compound 1 solved at 1.25 Å (PDB-ID: 5LIT) shows that the drug covers the minor groove of DNA, displaces bound water and interacts with neighbouring DNA molecules as a cross-linking agent. We conclude that 1 and 2 are powerful trypanocides that act directly on the kinetoplast, a structure unique to the order Kinetoplastida.

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Organizational Affiliation: 
• Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, 08019 Barcelona, Spain.
Instituto de Química Médica, IQM-CSIC, 28006 Madrid, Spain.
Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK.
The Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.42 kDa 
• Atom Count: 730 
• 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(*AP*AP*AP*TP*TP*T)-3')	A [auth D], B [auth C], C [auth A], D [auth B]	6	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6XV	E [auth D], G [auth C], J [auth B]	4-((4,5-dihydro-1H-imidazol-2-yl)amino)-N-(4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)benzamide dihydrochloride C19 H21 N7 O LDJIXMMIBFEFIF-UHFFFAOYSA-N
MG	F [auth D], H [auth C], I [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.121 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.123 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 22.33	α = 90
b = 40.25	β = 93.67
c = 72.423	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): Millan, C.R., Dardonville, C., de Koning, H.P., Saperas, N., Lourdes Campos, J.

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Funding Organization	Location	Grant Number
Government of Catalonia	Spain	2015 SGR 080

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 1.1: 2017-06-21
  Changes: Database references, Structure summary
• Version 1.2: 2017-06-28
  Changes: Database references, Structure summary
• Version 1.3: 2017-07-05
  Changes: Database references
• Version 1.4: 2017-09-06
  Changes: Database references
• Version 1.5: 2024-05-08
  Changes: Data collection, Database references, Derived calculations
• Version 1.6: 2026-03-04
  Changes: Refinement description, Structure summary