7V3T

Solution structure of thrombin binding aptamer G-quadruplex bound a self-adaptive small molecule with rotated ligands

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

  • Deposited: 2021-08-11 Released: 2022-09-28 
  • Deposition Author(s): Liu, W., Zhu, B.C., Mao, Z.W.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Solution structure of a thrombin binding aptamer complex with a non-planar platinum(ii) compound.

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

(2022) Chem Sci 13: 8371-8379

  • DOI: https://doi.org/10.1039/d2sc01196d
  • Primary Citation of Related Structures:  
    7V3T

  • PubMed Abstract: 

    Thrombin Binding Aptamer (TBA) is a monomolecular well-defined two G-tetrad antiparallel G-quadruplex DNA that inhibits the activity of human α-thrombin. In this report, we synthesized a quasi-cross-shaped platinum(ii) compound (L' 2 LPt) with one cyclometalated and two carbene ligands. We found L' 2 LPt has selective affinity to bind the TBA G-quadruplex. A fibrinogen clotting assay revealed that L' 2 LPt can abrogate the inhibitory activity of TBA against thrombin. We solved the 1 : 1 L' 2 LPt-TBA complex structure by NMR, which revealed a unique self-adaptive property of L' 2 LPt upon binding to TBA. In the complex, a carbene ligand of L' 2 LPt rotates to pair with the cyclometalated ligand to form a plane stacking over half of the TBA G-tetrad and covered by lateral TT loops. It is notable that the heavy atom Pt stays out of the G-tetrad. Meanwhile, the other carbene ligand remains relatively perpendicular and forms a hydrogen bond with a guanine to anchor the L' 2 LPt position. This structure exhibits a quasi-cross-shaped Pt(ii) compound bound to the G-quadruplex with an unusual "wall-mounted" binding mode. Our structures provide insights into the specific recognition of antiparallel G-quadruplex DNA by a self-adaptive Pt(ii) compound and useful information for the design of selective G-quadruplex targeting non-planar molecules.


  • Organizational Affiliation

    MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University Guangzhou 510275 China cesmzw@mail.sysu.edu.cn liuwenting@mail.sysu.edu.cn xiawei5@mail.sysu.edu.cn.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
TBA G4 DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')15Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5L1 (Subject of Investigation/LOI)
Query on 5L1

Download Ideal Coordinates CCD File 
B [auth A]11,13-bis(fluoranyl)-8-(1-methyl-3-pyridin-2-yl-imidazol-2-yl)-8-(1-methyl-3-pyridin-2-yl-imidazol-2-yl)-7$l^{4}-aza-8$l^{4}-platinatricyclo[7.4.0.0^{2,7}]trideca-1(9),2(7),3,5,10,12-hexaene
C29 H24 F2 N7 Pt
DJBNBBNLCQGCGN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • 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)21837006
National Natural Science Foundation of China (NSFC)91953117
National Natural Science Foundation of China (NSFC)21572282
National Natural Science Foundation of China (NSFC)22007103

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 1.1: 2022-12-21
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references