5W77

Complex of DNA and compounds

  • Classification: DNA/INHIBITOR
  • Organism(s): Homo sapiens

  • Deposited: 2017-06-19 Released: 2018-10-24 
  • Deposition Author(s): Chen, X., Walters, K.J.
  • Funding Organization(s): NIH, National Cancer Institute, Center for Cancer Research 

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


This is version 1.0 of the entry. See complete history

Literature

Chemical and structural studies provide a mechanistic basis for recognition of the MYC G-quadruplex.

Calabrese, D.R.Chen, X.Leon, E.C.Gaikwad, S.M.Phyo, Z.Hewitt, W.M.Alden, S.Hilimire, T.A.He, F.Michalowski, A.M.Simmons, J.K.Saunders, L.B.Zhang, S.Connors, D.Walters, K.J.Mock, B.A.Schneekloth Jr., J.S.

(2018) Nat Commun 9: 4229-4229

  • DOI: 10.1038/s41467-018-06315-w

  • PubMed Abstract: 
  • G-quadruplexes (G4s) are noncanonical DNA structures that frequently occur in the promoter regions of oncogenes, such as MYC, and regulate gene expression. Although G4s are attractive therapeutic targets, ligands capable of discriminating between dif ...

    G-quadruplexes (G4s) are noncanonical DNA structures that frequently occur in the promoter regions of oncogenes, such as MYC, and regulate gene expression. Although G4s are attractive therapeutic targets, ligands capable of discriminating between different G4 structures are rare. Here, we describe DC-34, a small molecule that potently downregulates MYC transcription in cancer cells by a G4-dependent mechanism. Inhibition by DC-34 is significantly greater for MYC than other G4-driven genes. We use chemical, biophysical, biological, and structural studies to demonstrate a molecular rationale for the recognition of the MYC G4. We solve the structure of the MYC G4 in complex with DC-34 by NMR spectroscopy and illustrate specific contacts responsible for affinity and selectivity. Modification of DC-34 reveals features required for G4 affinity, biological activity, and validates the derived NMR structure. This work advances the design of quadruplex-interacting small molecules to control gene expression in therapeutic areas such as cancer.


    Organizational Affiliation

    Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3')A22Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
9WP
Query on 9WP

Download SDF File 
Download CCD File 
A
4-[(azepan-1-yl)methyl]-5-hydroxy-2-methyl-N-[4-(trifluoromethyl)phenyl]-1-benzofuran-3-carboxamide
C24 H25 F3 N2 O3
CCAKHVBCBLIIEV-UHFFFAOYSA-N
 Ligand Interaction
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 or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NIH, National Cancer Institute, Center for Cancer ResearchUnited StatesIntramural Research Program

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release