6UJH | pdb_00006ujh

Discovery of fragment-inspired heterocyclic benzenesulfonamides as inhibitors of the WDR5-MYC interaction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 
    0.169 (Depositor), 0.168 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.146 (DCC) 
  • R-Value Observed: 
    0.148 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6UJH

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 69.69 kDa 
  • Atom Count: 6,050 
  • Modeled Residue Count: 626 
  • Deposited Residue Count: 626 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
WD repeat-containing protein 5
A, B
313Homo sapiensMutation(s): 0 
Gene Names: WDR5BIG3
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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QBS
(Subject of Investigation/LOI)

Query on QBS



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
(2R)-2-(4-chlorophenyl)-3-oxobutanenitrile
C10 H8 Cl N O
IPBZEJZUAZXNOS-SNVBAGLBSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
G [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS

Query on DMS



Download:Ideal Coordinates CCD File
H [auth B],
I [auth B],
J [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free:  0.169 (Depositor), 0.168 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.146 (DCC) 
  • R-Value Observed: 0.148 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.135α = 89.98
b = 47.274β = 90.5
c = 68.542γ = 104.35
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States--

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: 2023-10-11
    Changes: Data collection, Database references, Refinement description