6LNZ

NMR solution structure of VEGF G-quadruplex bound a non-planar cyclometalated-carbene platinum(II) complex

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

  • Deposited: 2020-01-02 Released: 2021-01-13 
  • Deposition Author(s): Liu, W., Zhu, B.Z., Mao, Z.W.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


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Literature

Selectivity and Targeting of G-Quadruplex Binders Activated by Adaptive Binding and Controlled by Chemical Kinetics.

Zhu, B.C.He, J.Liu, W.Xia, X.Y.Liu, L.Y.Liang, B.B.Yao, H.G.Liu, B.Ji, L.N.Mao, Z.W.

(2021) Angew Chem Int Ed Engl 60: 15340-15343

  • DOI: https://doi.org/10.1002/anie.202104624
  • Primary Citation of Related Structures:  
    6LNZ

  • PubMed Abstract: 

    G-quadruplexes (G4s) are prevalent in oncogenes and are potential antitumor drug targets. However, binding selectivity of compounds to G4s still faces challenges. Herein, we report a platinum(II) complex (Pt1), whose affinity to G4-DNA is activated by adaptive binding and selectivity controlled by binding kinetics. The resolved structure of Pt1/VEGF-G4 (a promoter G4) shows that Pt1 matches 3'-G-tetrad of VEGF-G4 through Cl - -dissociation and loop rearrangement of VEGF-G4. Binding rate constants are determined by coordination bond breakage/formation, correlating fully with affinities. The selective rate-determining binding step, Cl - -dissociation upon G4-binding, is 2-3 orders of magnitude higher than dsDNA. Pt1 potently targets G4 in living cells, effectively represses VEGF expression, and inhibits vascular growth in zebrafish. We show adaptive G4-binding activation and controlled by kinetics, providing a complementary design principle for compounds targeting G4 or similar biomolecules.


  • Organizational Affiliation

    MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, State Key Laboratory of Oncology in South China, Sun Yat-Sen University, No. 135, Xingang Xi Road, 510275, Guangzhou, China.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*GP*GP*GP*CP*GP*GP*GP*CP*CP*TP*TP*GP*GP*GP*CP*GP*GP*GP*GP*T)-3')22Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EL9 (Subject of Investigation/LOI)
Query on EL9

Download Ideal Coordinates CCD File 
B [auth A]cyclometalated-carbene platinum(II) complex
C20 H15 F2 N4 Pt
MSOPGFNQFJYXDN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21837006

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references