6JWD | pdb_00006jwd

structure of RET G-quadruplex in complex with berberine

• PDB DOI: https://doi.org/10.2210/pdb6JWD/pdb
• NAKB: 6JWD

• Classification: DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2019-04-19 Released: 2020-04-22 
• Deposition Author(s): Wang, F., Wang, C., Liu, Y., Lan, W.X., Li, Y.M., Wang, R.X., Cao, C.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Colchicine selective interaction with oncogene RET G-quadruplex revealed by NMR.

Wang, F., Wang, C., Liu, Y., Lan, W., Han, H., Wang, R., Huang, S., Cao, C.

(2020) Chem Commun (Camb) 56: 2099-2102

• PubMed: 32025680 
• DOI: https://doi.org/10.1039/d0cc00221f
• Primary Citation Related Structures: 
  6JWD, 6JWE


• PubMed Abstract: 
  

  G-quadruplexes (G4s) are frequently formed in the promoter regions of oncogenes, considered as promising drug targets for anticancer therapy. Due to high structure similarity of G4s, discovering ligands selectively interacting with only one G4 is extremely difficult. Here, mainly by NMR, we report that colchicine selectively binds to oncogene RET G4-DNA.

---

Organizational Affiliation: 
• State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China. [e-mail] and University of Chinese Academy of Science, No. 19A, Yuquan Road, Shijingshan District, Beijing, 100049, China.
Institute of Drug Discovery Technology, Ningbo University, No. 818 Fenghua Road, Ningbo, Zhejiang 315211, China.
State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China. [e-mail] and University of Chinese Academy of Science, No. 19A, Yuquan Road, Shijingshan District, Beijing, 100049, China and Institute of Drug Discovery Technology, Ningbo University, No. 818 Fenghua Road, Ningbo, Zhejiang 315211, China.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.73 kDa 
• Atom Count: 451 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*GP*GP*CP*GP*GP*GP*GP*CP*GP*GP*GP*GP*CP*GP*GP*GP*GP*T)-3')	A	20	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BER (Subject of Investigation/LOI)	B [auth A]	BERBERINE C20 H18 N O4 YBHILYKTIRIUTE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-22 
Deposition Author(s): Wang, F., Wang, C., Liu, Y., Lan, W.X., Li, Y.M., Wang, R.X., Cao, C.

Revision History  

• Version 1.0: 2020-04-22
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Database references, Other
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references