Complex of tetra-(4-n-methylpyridyl) porphin with monomeric parallel-stranded DNA tetraplex, snap-back 3+1 3' G-tetrad, single-residue chain reversal loops, GAG triad in the context of GAAG diagonal loop, C-MYC promoter, NMR, 6 struct.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter.

Phan, A.T.Kuryavyi, V.Gaw, H.Y.Patel, D.J.

(2005) Nat Chem Biol 1: 167-173

  • DOI: https://doi.org/10.1038/nchembio723
  • Primary Citation of Related Structures:  
    2A5P, 2A5R

  • PubMed Abstract: 

    It has been widely accepted that DNA can adopt other biologically relevant structures beside the Watson-Crick double helix. One recent important example is the guanine-quadruplex (G-quadruplex) structure formed by guanine tracts found in the MYC (or c-myc) promoter region, which regulates the transcription of the MYC oncogene. Stabilization of this G-quadruplex by ligands, such as the cationic porphyrin TMPyP4, decreases the transcriptional level of MYC. Here, we report the first structure of a DNA fragment containing five guanine tracts from this region. An unusual G-quadruplex fold, which was derived from NMR restraints using unambiguous model-independent resonance assignment approaches, involves a core of three stacked guanine tetrads formed by four parallel guanine tracts with all anti guanines and a snapback 3'-end syn guanine. We have determined the structure of the complex formed between this G-quadruplex and TMPyP4. This structural information, combined with details of small-molecule interaction, provides a platform for the design of anticancer drugs targeting multi-guanine-tract sequences that are found in the MYC and other oncogenic promoters, as well as in telomeres.

  • Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA. phantuan@mskcc.org


Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on POH

Download Ideal Coordinates CCD File 
B [auth A](1Z,4Z,9Z,15Z)-5,10,15,20-tetrakis(1-methylpyridin-1-ium-4-yl)-21,23-dihydroporphyrin
C44 H38 N8
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance