7N3U | pdb_00007n3u

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

• PDB DOI: https://doi.org/10.2210/pdb7N3U/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2021-06-02 Released: 2021-09-01 
• Deposition Author(s): Lee, C.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.267 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

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

• PubMed: 34423975 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c01121
• Primary Citation 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.

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Organizational Affiliation: 
• Zentalis Pharmaceuticals, San Diego, California 92121, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.7 kDa 
• Atom Count: 2,146 
• Modeled Residue Count: 261 
• Deposited Residue Count: 285 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Wee1-like protein kinase	A	285	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
05J (Subject of Investigation/LOI)	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

Binding Affinity Annotations
ID	Source	Binding Affinity
05J	BindingDB:  7N3U	IC50: min: 55, max: 567 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.267 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.92	α = 90
b = 50.51	β = 90
c = 119.58	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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