2MB3 | pdb_00002mb3

Solution structure of an intramolecular (3+1) human telomeric G-quadruplex bound to a telomestatin derivative

• PDB DOI: https://doi.org/10.2210/pdb2MB3/pdb
• NAKB: 2MB3
• BMRB: 19387

• Classification: DNA/DNA INHIBITOR
• Mutation(s): No 


• Deposited: 2013-07-24 Released: 2013-08-28 
• Deposition Author(s): Chung, W.J., Heddi, B., Tera, M., Iida, K., Nagasawa, K., Phan, A.T.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure of an intramolecular (3 + 1) human telomeric g-quadruplex bound to a telomestatin derivative.

Chung, W.J., Heddi, B., Tera, M., Iida, K., Nagasawa, K., Phan, A.T.

(2013) J Am Chem Soc 135: 13495-13501

• PubMed: 23909929 
• DOI: https://doi.org/10.1021/ja405843r
• Primary Citation Related Structures: 
  2MB3


• PubMed Abstract: 
  

  Guanine-rich human telomeric DNA can adopt secondary structures known as G-quadruplexes, which can be targeted by small molecules to achieve anticancer effects. So far, the structural information on complexes between human telomeric DNA and ligands is limited to the parallel G-quadruplex conformation, despite the high structural polymorphism of human telomeric G-quadruplexes. No structure has been yet resolved for the complex with telomestatin, one of the most promising G-quadruplex-targeting anticancer drug candidates. Here we present the first high-resolution structure of the complex between an intramolecular (3 + 1) human telomeric G-quadruplex and a telomestatin derivative, the macrocyclic hexaoxazole L2H2-6M(2)OTD. This compound is observed to interact with the G-quadruplex through π-stacking and electrostatic interactions. This structural information provides a platform for the design of topology-specific G-quadruplex-targeting compounds and is valuable for the development of new potent anticancer drugs.

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Organizational Affiliation: 
• School of Physical and Mathematical Sciences, Nanyang Technological University , Singapore.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.28 kDa 
• Atom Count: 555 
• 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*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')	A	24	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L2H	B [auth A]	(12S,27S)-12,27-bis(4-aminobutyl)-4,30-dimethyl-3,7,14,18,22,29-hexaoxa-11,26,31,32,33,34,35,36-octaazaheptacyclo[26.2. 1.1~2,5~.1~6,9~.1~13,16~.1~17,20~.1~21,24~]hexatriaconta-1(30),2(36),4,6(35),8,13(34),15,17(33),19,21(32),23,28(31)-dode caene-10,25-dione C32 H34 N10 O8 VFOYOVBIUSPROZ-ROUUACIJSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Chung, W.J., Heddi, B., Tera, M., Iida, K., Nagasawa, K., Phan, A.T.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2013-09-25
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references