6UHY | pdb_00006uhy

WDR5 in complex with Myc site fragment inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 
    0.181 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.155 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Q8GClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Discovery of WD Repeat-Containing Protein 5 (WDR5)-MYC Inhibitors Using Fragment-Based Methods and Structure-Based Design.

Chacon Simon, S.Wang, F.Thomas, L.R.Phan, J.Zhao, B.Olejniczak, E.T.Macdonald, J.D.Shaw, J.G.Schlund, C.Payne, W.Creighton, J.Stauffer, S.R.Waterson, A.G.Tansey, W.P.Fesik, S.W.

(2020) J Med Chem 63: 4315-4333

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00224
  • Primary Citation of Related Structures:  
    6UHY, 6UHZ, 6UIF, 6UIK, 6UJ4, 6UJH, 6UJJ, 6UJL, 6UOZ

  • PubMed Abstract: 

    The frequent deregulation of MYC and its elevated expression via multiple mechanisms drives cells to a tumorigenic state. Indeed, MYC is overexpressed in up to ∼50% of human cancers and is considered a highly validated anticancer target. Recently, we discovered that WD repeat-containing protein 5 (WDR5) binds to MYC and is a critical cofactor required for the recruitment of MYC to its target genes and reported the first small molecule inhibitors of the WDR5-MYC interaction using structure-based design. These compounds display high binding affinity, but have poor physicochemical properties and are hence not suitable for in vivo studies. Herein, we conducted an NMR-based fragment screening to identify additional chemical matter and, using a structure-based approach, we merged a fragment hit with the previously reported sulfonamide series. Compounds in this series can disrupt the WDR5-MYC interaction in cells, and as a consequence, we observed a reduction of MYC localization to chromatin.


  • Organizational Affiliation

    Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
WDR5
A, B
304Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens)
Explore P61964 
Go to UniProtKB:  P61964
PHAROS:  P61964
GTEx:  ENSG00000196363 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61964
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
Q8G BindingDB:  6UHY Kd: 2.00e+7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free:  0.181 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.155 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.464α = 90
b = 46.955β = 117.63
c = 112.77γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Q8GClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references