6PG4

WDR5delta32 bound to (2-methyl-1H-imidazol-4-yl)methanol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Fragment screening for a protein-protein interaction inhibitor to WDR5.

Dennis, M.L.Morrow, B.J.Dolezal, O.Cuzzupe, A.N.Stupple, A.E.Newman, J.Bentley, J.Hattarki, M.Nuttall, S.D.Foitzik, R.C.Street, I.P.Stupple, P.A.Monahan, B.J.Peat, T.S.

(2019) Struct Dyn. 6: 064701-064701

  • DOI: 10.1063/1.5122849
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The WD40-repeat protein WDR5 scaffolds various epigenetic writers and is a critical component of the mammalian SET/MLL histone methyltransferase complex. Dysregulation of the MLL1 catalytic function is associated with mixed-lineage leukemia, and anta ...

    The WD40-repeat protein WDR5 scaffolds various epigenetic writers and is a critical component of the mammalian SET/MLL histone methyltransferase complex. Dysregulation of the MLL1 catalytic function is associated with mixed-lineage leukemia, and antagonism of the WDR5-MLL1 interaction by small molecules has been proposed as a therapeutic strategy for MLL-rearranged cancers. Small molecule binders of the "WIN" site of WDR5 that cause displacement from chromatin have been additionally implicated to be of broader use in cancer treatment. In this study, a fragment screen with Surface Plasmon Resonance (SPR) was used to identify a highly ligand-efficient imidazole-containing compound that is bound in the WIN site. The subsequent medicinal chemistry campaign-guided by a suite of high-resolution cocrystal structures with WDR5-progressed the initial hit to a low micromolar binder. One outcome from this study is a moiety that substitutes well for the side chain of arginine; a tripeptide containing one such substitution was resolved in a high resolution structure (1.5 Å) with a binding mode analogous to the native tripeptide. SPR furthermore indicates a similar residence time ( k d = ∼0.06 s -1 ) for these two analogs. This novel scaffold therefore represents a possible means to overcome the potential permeability issues of WDR5 ligands that possess highly basic groups like guanidine. The series reported here furthers the understanding of the WDR5 WIN site and functions as a starting point for the development of more potent WDR5 inhibitors that may serve as cancer therapeutics.


    Organizational Affiliation

    Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria 3052, Australia.,SYNthesis med chem (Australia) Pty Ltd, Bio21 Institute, 30 Flemington Road, Parkville, Victoria 3052, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
WD repeat-containing protein 5
A
305Homo sapiensMutation(s): 0 
Gene Names: WDR5 (BIG3)
Find proteins for P61964 (Homo sapiens)
Go to Gene View: WDR5
Go to UniProtKB:  P61964
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OHG
Query on OHG

Download SDF File 
Download CCD File 
A
(2-methyl-1H-imidazol-4-yl)methanol
C5 H8 N2 O
MQRMTENGXFRETM-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.754α = 90.00
b = 65.305β = 90.00
c = 97.214γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-12-11
    Type: Initial release