2KVY

NMR solution structure of the 4:1 complex between an uncharged distamycin A analogue and [d(TGGGGT)]4


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and conformational requisites in DNA quadruplex groove binding: another piece to the puzzle.

Cosconati, S.Marinelli, L.Trotta, R.Virno, A.De Tito, S.Romagnoli, R.Pagano, B.Limongelli, V.Giancola, C.Baraldi, P.G.Mayol, L.Novellino, E.Randazzo, A.

(2010) J.Am.Chem.Soc. 132: 6425-6433

  • DOI: 10.1021/ja1003872

  • PubMed Abstract: 
  • The study of DNA G-quadruplex stabilizers has enjoyed a great momentum in the late years due to their application as anticancer agents. The recognition of the grooves of these structural motifs is expected to result in a higher degree of selectivity ...

    The study of DNA G-quadruplex stabilizers has enjoyed a great momentum in the late years due to their application as anticancer agents. The recognition of the grooves of these structural motifs is expected to result in a higher degree of selectivity over other DNA structures. Therefore, to achieve an enhanced knowledge on the structural and conformational requisites for quadruplex groove recognition, distamycin A, the only compound for which a pure groove binding has been proven, has been chemically modified. Surprisingly, structural and thermodynamic studies revealed that the absence of Coulombic interactions results in an unprecedented binding position in which both the groove and the 3' end of the DNA are occupied. This further contribution adds another piece to the so far elusive puzzle of the recognition between ligands and DNA quadruplexes and will serve as a platform for a rational design of new groove binders.


    Organizational Affiliation

    Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli Federico II, via D. Montesano 49, I-80131 Napoli, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')A,B,C,D6N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KVY
Query on KVY

Download SDF File 
Download CCD File 
A, B, C, D
4-amino-1-methyl-N-{1-methyl-5-[(1-methyl-5-{[3-(methylamino)-3-oxopropyl]carbamoyl}-1H-pyrrol-3-yl)carbamoyl]-1H-pyrrol-3-yl}-1H-pyrrole-2-carboxamide
C22 H28 N8 O4
HXPHNDLDCCQYDB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance