8UJY | pdb_00008ujy

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)

• PDB DOI: https://doi.org/10.2210/pdb8UJY/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-10-11 Released: 2023-12-20 
• Deposition Author(s): Zhao, B., Amporndanai, K., Fesik, S.W.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.232 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 

Starting Model: experimental

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

• PubMed: 38085679 
• DOI: https://doi.org/10.1021/acs.jmedchem.3c01529
• Primary Citation 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.

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Organizational Affiliation: 
• Molecular Design and Synthesis Center, Vanderbilt Institute of Chemical Biology, Nashville, Tennessee 37232-0142, United States.
Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States.
Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701-4907, United States.
Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232-0142, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.64 kDa 
• Atom Count: 5,216 
• Modeled Residue Count: 611 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 5	A, B	312	Homo sapiens	Mutation(s): 0  Gene Names: WDR5, BIG3
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens) Explore P61964  Go to UniProtKB:  P61964
PHAROS:  P61964 GTEx:  ENSG00000196363

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VV3 (Subject of Investigation/LOI)	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 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.81	α = 88.04
b = 47.68	β = 89.27
c = 68.869	γ = 74.66

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Zhao, B., Amporndanai, K., Fesik, S.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	HHSN261200800001E

Revision History  

• 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