6E22

Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with picomolar affinity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Displacement of WDR5 from Chromatin by a WIN Site Inhibitor with Picomolar Affinity.

Aho, E.R.Wang, J.Gogliotti, R.D.Howard, G.C.Phan, J.Acharya, P.Macdonald, J.D.Cheng, K.Lorey, S.L.Lu, B.Wenzel, S.Foshage, A.M.Alvarado, J.Wang, F.Shaw, J.G.Zhao, B.Weissmiller, A.M.Thomas, L.R.Vakoc, C.R.Hall, M.D.Hiebert, S.W.Liu, Q.Stauffer, S.R.Fesik, S.W.Tansey, W.P.

(2019) Cell Rep 26: 2916-2928.e13

  • DOI: 10.1016/j.celrep.2019.02.047
  • Primary Citation of Related Structures:  
    6DY7, 6DYA, 6E1Y, 6E1Z, 6E22, 6E23

  • PubMed Abstract: 
  • The chromatin-associated protein WDR5 is a promising target for pharmacological inhibition in cancer. Drug discovery efforts center on the blockade of the "WIN site" of WDR5, a well-defined pocket that is amenable to small molecule inhibition. Various cancer contexts have been proposed to be targets for WIN site inhibitors, but a lack of understanding of WDR5 target genes and of the primary effects of WIN site inhibitors hampers their utility ...

    The chromatin-associated protein WDR5 is a promising target for pharmacological inhibition in cancer. Drug discovery efforts center on the blockade of the "WIN site" of WDR5, a well-defined pocket that is amenable to small molecule inhibition. Various cancer contexts have been proposed to be targets for WIN site inhibitors, but a lack of understanding of WDR5 target genes and of the primary effects of WIN site inhibitors hampers their utility. Here, by the discovery of potent WIN site inhibitors, we demonstrate that the WIN site links WDR5 to chromatin at a small cohort of loci, including a specific subset of ribosome protein genes. WIN site inhibitors rapidly displace WDR5 from chromatin and decrease the expression of associated genes, causing translational inhibition, nucleolar stress, and p53 induction. Our studies define a mode by which WDR5 engages chromatin and forecast that WIN site blockade could have utility against multiple cancer types.


    Organizational Affiliation

    Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA. Electronic address: william.p.tansey@vanderbilt.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
WD repeat-containing protein 5A, B313Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HLS (Subject of Investigation/LOI)
Query on HLS

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]3-{[(4,5-dihydro-1H-imidazol-2-yl)amino]methyl}-N-[(3,5-dimethoxyphenyl)methyl]-4-fluorobenzamide
C20 H23 F N4 O3
VDAMWMOTTUWVPR-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
HLS Binding MOAD:  6E22 Kd: 1.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.684α = 108.03
b = 53.635β = 90.15
c = 65.31γ = 106.27
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-07-10 
  • Released Date: 2019-03-13 
  • Deposition Author(s): Phan, J., Fesik, S.W.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesWDR5-MLL1 NExT Leidos Biomedical Research 16X117 HHSN2162008000 01E UNIV 57992

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence