6UFX | pdb_00006ufx

WD repeat-containing protein 5 complexed with N-[(3,5-dimethoxyphenyl)methyl]-4'-fluoro-5-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}-2'-methyl[1,1'-biphenyl]-3-carboxamide (compound 13)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 
    0.208 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6UFX

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Discovery and Structure-Based Optimization of Potent and Selective WD Repeat Domain 5 (WDR5) Inhibitors Containing a Dihydroisoquinolinone Bicyclic Core.

Tian, J.Teuscher, K.B.Aho, E.R.Alvarado, J.R.Mills, J.J.Meyers, K.M.Gogliotti, R.D.Han, C.Macdonald, J.D.Sai, J.Shaw, J.G.Sensintaffar, J.L.Zhao, B.Rietz, T.A.Thomas, L.R.Payne, W.G.Moore, W.J.Stott, G.M.Kondo, J.Inoue, M.Coffey, R.J.Tansey, W.P.Stauffer, S.R.Lee, T.Fesik, S.W.

(2020) J Med Chem 63: 656-675

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01608
  • Primary Citation Related Structures: 
    6UCS, 6UFX

  • PubMed Abstract: 

    WD repeat domain 5 (WDR5) is a member of the WD40-repeat protein family that plays a critical role in multiple chromatin-centric processes. Overexpression of WDR5 correlates with a poor clinical outcome in many human cancers, and WDR5 itself has emerged as an attractive target for therapy. Most drug-discovery efforts center on the WIN site of WDR5 that is responsible for the recruitment of WDR5 to chromatin. Here, we describe discovery of a novel WDR5 WIN site antagonists containing a dihydroisoquinolinone bicyclic core using a structure-based design. These compounds exhibit picomolar binding affinity and selective concentration-dependent antiproliferative activities in sensitive MLL-fusion cell lines. Furthermore, these WDR5 WIN site binders inhibit proliferation in MYC-driven cancer cells and reduce MYC recruitment to chromatin at MYC/WDR5 co-bound genes. Thus, these molecules are useful probes to study the implication of WDR5 inhibition in cancers and serve as a potential starting point toward the discovery of anti-WDR5 therapeutics.


  • Organizational Affiliation
    • Leidos Biomedical Research , Frederick National Laboratory for Cancer Research , Frederick , Maryland 21701 , United States.

Macromolecule Content 

  • Total Structure Weight: 33.84 kDa 
  • Atom Count: 2,454 
  • Modeled Residue Count: 303 
  • Deposited Residue Count: 303 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
WD repeat-containing protein 5303Homo 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
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q6S
(Subject of Investigation/LOI)

Query on Q6S



Download:Ideal Coordinates CCD File
B [auth A]N-[(3,5-dimethoxyphenyl)methyl]-4'-fluoro-5-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}-2'-methyl[1,1'-biphenyl]-3-carboxamide
C28 H29 F N4 O3
PSABMKXBOJUOBD-SJCQXOIGSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free:  0.208 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.625α = 90
b = 98.896β = 90
c = 80.546γ = 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 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesHHSN261200800001E
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA200709
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA68485

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-01
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Database references
  • Version 1.2: 2020-02-05
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description