6DAS

Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery of Potent 2-Aryl-6,7-dihydro-5 H-pyrrolo[1,2- a]imidazoles as WDR5-WIN-Site Inhibitors Using Fragment-Based Methods and Structure-Based Design.

Wang, F.Jeon, K.O.Salovich, J.M.Macdonald, J.D.Alvarado, J.Gogliotti, R.D.Phan, J.Olejniczak, E.T.Sun, Q.Wang, S.Camper, D.Yuh, J.P.Shaw, J.G.Sai, J.Rossanese, O.W.Tansey, W.P.Stauffer, S.R.Fesik, S.W.

(2018) J. Med. Chem. 61: 5623-5642

  • DOI: 10.1021/acs.jmedchem.8b00375
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • WDR5 is a chromatin-regulatory scaffold protein overexpressed in various cancers and a potential epigenetic drug target for the treatment of mixed-lineage leukemia. Here, we describe the discovery of potent and selective WDR5-WIN-site inhibitors usin ...

    WDR5 is a chromatin-regulatory scaffold protein overexpressed in various cancers and a potential epigenetic drug target for the treatment of mixed-lineage leukemia. Here, we describe the discovery of potent and selective WDR5-WIN-site inhibitors using fragment-based methods and structure-based design. NMR-based screening of a large fragment library identified several chemically distinct hit series that bind to the WIN site within WDR5. Members of a 6,7-dihydro-5 H-pyrrolo[1,2- a]imidazole fragment class were expanded using a structure-based design approach to arrive at lead compounds with dissociation constants <10 nM and micromolar cellular activity against an AML-leukemia cell line. These compounds represent starting points for the discovery of clinically useful WDR5 inhibitors for the treatment of cancer.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
WD repeat-containing protein 5
A, B
313Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G2D
Query on G2D

Download SDF File 
Download CCD File 
A, B
N-[(1R)-6-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)-2,3-dihydro-1H-inden-1-yl]-3-methoxy-4-methylbenzamide
C24 H25 N3 O2
PHINNLAJTUGZSZ-HXUWFJFHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.177 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 46.662α = 71.85
b = 53.709β = 89.86
c = 65.352γ = 73.82
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-05-01 
  • Released Date: 2018-07-18 
  • Deposition Author(s): Phan, J., Fesik, S.W.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesWDR5-MLL1 NExT Leidos Biomedical Research 16X117 HHSN2162008000 01E UNIV 57992

Revision History 

  • Version 1.0: 2018-07-18
    Type: Initial release