8BJU | pdb_00008bju

HUMAN WEE1 KINASE IN COMPLEX WITH INHIBITOR 1-[6-(1-Hydroxy-1-methyl-ethyl)-pyridin-2-yl]-2-(2-methoxy-phenyl)-6-[4-(4-methyl-piperazin-1-yl)-phenylamino]-1,2-dihydro-pyrazolo[3,4-d]pyrimidin-3-one

• PDB DOI: https://doi.org/10.2210/pdb8BJU/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2022-11-06 Released: 2023-05-31 
• Deposition Author(s): Musil, D., Lan, R.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.263 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Selective Wee1 Inhibitors Led to Antitumor Activity In Vitro and Correlated with Myelosuppression.

Guler, S., DiPoto, M.C., Crespo, A., Caldwell, R., Doerfel, B., Grossmann, N., Ho, K., Huck, B., Jones, C.C., Lan, R., Musil, D., Potnick, J., Schilke, H., Sherer, B., Simon, S., Sirrenberg, C., Zhang, Z., Liu-Bujalski, L.

(2023) ACS Med Chem Lett 14: 566-576

• PubMed: 37197456 
• DOI: https://doi.org/10.1021/acsmedchemlett.2c00481
• Primary Citation Related Structures: 
  8BJT, 8BJU


• PubMed Abstract: 
  

  Wee1 is a tyrosine kinase that is highly expressed in several cancer types. Wee1 inhibition can lead to suppression of tumor cell proliferation and sensitization of cells to the effects of DNA-damaging agents. AZD1775 is a nonselective Wee1 inhibitor for which myelosuppression has been observed as a dose-limiting toxicity. We have applied structure-based drug design (SBDD) to rapidly generate highly selective Wee1 inhibitors that demonstrate better selectivity than AZD1775 against PLK1, which is known to cause myelosuppression (including thrombocytopenia) when inhibited. While selective Wee1 inhibitors described herein still achieved in vitro antitumor efficacy, thrombocytopenia was still observed in vitro .

---

Organizational Affiliation: 
• EMD Serono, Billerica, Massachusetts 01821, United States.
Merck Healthcare KGaA, 64293 Darmstadt, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.74 kDa 
• Atom Count: 2,333 
• Modeled Residue Count: 260 
• 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
QT9 (Subject of Investigation/LOI)	B [auth A]	2-(2-methoxyphenyl)-6-[[4-(4-methylpiperazin-1-yl)phenyl]amino]-1-[6-(2-oxidanylpropan-2-yl)pyridin-2-yl]pyrazolo[3,4-d]pyrimidin-3-one C31 H34 N8 O3 YRSUINBEIRGTSA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
QT9	BindingDB:  8BJU	IC50: min: 9.6, max: 542 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.263 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.622	α = 90
b = 50.577	β = 90
c = 117.57	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-31 
Deposition Author(s): Musil, D., Lan, R.

---

Funding Organization	Location	Grant Number
Not funded	Germany	--

Revision History  

• Version 1.0: 2023-05-31
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description