2KVY | pdb_00002kvy

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

• PDB DOI: https://doi.org/10.2210/pdb2KVY/pdb
• NAKB: 2KVY

• Classification: DNA
• Mutation(s): No 


• Deposited: 2010-03-29 Released: 2010-05-26 
• Deposition Author(s): Cosconati, S., Marinelli, L., Trotta, R., Virno, A., De Tito, S., Romagnoli, R., Pagano, B., Limongelli, V., Giancola, C., Baraldi, P., Mayol, L., Novellino, E., Randazzo, A.

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Experimental Data Snapshot

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

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

• PubMed: 20394365 
• DOI: https://doi.org/10.1021/ja1003872
• Primary Citation Related Structures: 
  2KVY


• 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 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.

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

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.4 kDa 
• Atom Count: 636 
• 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(*TP*GP*GP*GP*GP*T)-3')	A, B, C, D	6	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KVY	E [auth A], F [auth B], G [auth C], H [auth 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

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-26 
Deposition Author(s): Cosconati, S., Marinelli, L., Trotta, R., Virno, A., De Tito, S., Romagnoli, R., Pagano, B., Limongelli, V., Giancola, C., Baraldi, P., Mayol, L., Novellino, E., Randazzo, A.

Revision History  

• Version 1.0: 2010-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-05-22
  Changes: Data collection