6GIM

Structure of the DNA duplex d(AAATTT)2 with [N-(3-chloro-4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)-4-((4,5-dihydro-1H-imidazol-2- yl)amino)benzamide] - (drug JNI18)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.0 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
  • Primary Citation of Related Structures:  

  • 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,B6Trypanosoma brucei
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EZK
Query on EZK

Download SDF File 
Download CCD File 
B, C, D
[4-[(3-chloranyl-4-imidazolidin-2-ylideneazaniumyl-phenyl)carbamoyl]phenyl]-imidazolidin-2-ylidene-azanium
C19 H22 Cl N7 O
RZRDBTPEIPCUHV-UHFFFAOYSA-P
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.143 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 22.630α = 90.00
b = 40.470β = 93.91
c = 72.255γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
REFMACrefinement
MOLREPphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainSAF2015-66690-R
Spanish Ministry of Economy and CompetitivenessSpainBFU2009-10380
Spanish Ministry of Economy and CompetitivenessSpainFPU12/04824, EST14/00449
Wellcome TrustUnited Kingdom085349

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release