7N3U

Crystal structure of human WEE1 kinase domain in complex with ZN-c3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

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Literature

Discovery of ZN-c3, a Highly Potent and Selective Wee1 Inhibitor Undergoing Evaluation in Clinical Trials for the Treatment of Cancer.

Huang, P.Q., Boren, B.C., Hegde, S.G., Liu, H., Unni, A.K., Abraham, S., Hopkins, C.D., Paliwal, S., Samatar, A.A., Li, J., Bunker, K.D.

(2021) J Med Chem 64: 13004-13024

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01121
  • Primary Citation of Related Structures:  
    7N3U

  • PubMed Abstract: 

    Wee1 inhibition has received great attention in the past decade as a promising therapy for cancer treatment. Therefore, a potent and selective Wee1 inhibitor is highly desirable. Our efforts to make safer and more efficacious Wee1 inhibitors led to the discovery of compound 16 , a highly selective Wee1 inhibitor with balanced potency, ADME, and pharmacokinetic properties. The chiral ethyl moiety of compound 16 provided an unexpected improvement of Wee1 potency. Compound 16 , known as ZN-c3, showed excellent in vivo efficacy and is currently being evaluated in phase 2 clinical trials.

    • Organizational Affiliation: 

    Zentalis Pharmaceuticals, San Diego, California 92121, United States.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Wee1-like protein kinase285Homo sapiensMutation(s): 0 
Gene Names: WEE1
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P30291 (Homo sapiens)
Explore P30291 
Go to UniProtKB:  P30291
PHAROS:  P30291
GTEx:  ENSG00000166483 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30291
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
05J (Subject of Investigation/LOI)
Query on 05J
Download Ideal Coordinates CCD File 
B [auth A]1-[(7R)-7-ethyl-7-hydroxy-6,7-dihydro-5H-cyclopenta[b]pyridin-2-yl]-6-[4-(4-methylpiperazin-1-yl)anilino]-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one
C29 H34 N8 O2
OXTSYWDBUVRXFF-GDLZYMKVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.92α = 90
b = 50.51β = 90
c = 119.58γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2021-09-01 
    • Deposition Author(s): Lee, C.C.

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2021-09-22
    Changes: Database references
  • Version 2.0: 2022-04-13
    Changes: Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-10-18
    Changes: Data collection, Refinement description