5LIT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.121 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

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

  • DOI: 10.1093/nar/gkx521

  • 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 ...

    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.


    Organizational Affiliation

    Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, 08019 Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*AP*TP*TP*T)-3')D,C,A,B6synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6XV
Query on 6XV

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Download CCD File 
B, C, D
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
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.121 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 22.330α = 90.00
b = 40.250β = 93.67
c = 72.423γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Government of CataloniaSpain2015 SGR 080

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-06-21
    Type: Database references, Structure summary
  • Version 1.2: 2017-06-28
    Type: Database references, Structure summary
  • Version 1.3: 2017-07-05
    Type: Database references
  • Version 1.4: 2017-09-06
    Type: Database references