8UJY

Crystal structure of human WD repeat-containing protein 5 in complex with 4-(3,5-dimethoxybenzyl)-9-(4-fluoro-2-methylphenyl)-7-((2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl)methyl)-3,4-dihydrobenzo[f][1,4]oxazepin-5(2H)-one (compound 8)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.188 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-Based Discovery of Potent, Orally Bioavailable Benzoxazepinone-Based WD Repeat Domain 5 Inhibitors.

Teuscher, K.B.Mills, J.J.Tian, J.Han, C.Meyers, K.M.Sai, J.South, T.M.Crow, M.M.Van Meveren, M.Sensintaffar, J.L.Zhao, B.Amporndanai, K.Moore, W.J.Stott, G.M.Tansey, W.P.Lee, T.Fesik, S.W.

(2023) J Med Chem 66: 16783-16806

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01529
  • Primary Citation of Related Structures:  
    8UJY

  • PubMed Abstract: 

    The chromatin-associated protein WDR5 (WD repeat domain 5) is an essential cofactor for MYC and a conserved regulator of ribosome protein gene transcription. It is also a high-profile target for anti-cancer drug discovery, with proposed utility against both solid and hematological malignancies. We have previously discovered potent dihydroisoquinolinone-based WDR5 WIN-site inhibitors with demonstrated efficacy and safety in animal models. In this study, we sought to optimize the bicyclic core to discover a novel series of WDR5 WIN-site inhibitors with improved potency and physicochemical properties. We identified the 3,4-dihydrobenzo[ f ][1,4]oxazepin-5(2 H )-one core as an alternative scaffold for potent WDR5 inhibitors. Additionally, we used X-ray structural analysis to design partially saturated bicyclic P 7 units. These benzoxazepinone-based inhibitors exhibited increased cellular potency and selectivity and favorable physicochemical properties compared to our best-in-class dihydroisoquinolinone-based counterparts. This study opens avenues to discover more advanced WDR5 WIN-site inhibitors and supports their development as novel anti-cancer therapeutics.


  • Organizational Affiliation

    Molecular Design and Synthesis Center, Vanderbilt Institute of Chemical Biology, Nashville, Tennessee 37232-0142, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 5
A, B
312Homo 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
VV3 (Subject of Investigation/LOI)
Query on VV3

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(9P)-4-[(3,5-dimethoxyphenyl)methyl]-9-(4-fluoro-2-methylphenyl)-7-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}-3,4-dihydro-1,4-benzoxazepin-5(2H)-one
C30 H31 F N4 O4
KLFBZLMEAVVEOS-NHQGMKOOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.188 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.81α = 88.04
b = 47.68β = 89.27
c = 68.869γ = 74.66
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Database references