3BIZ

Wee1 kinase complex with inhibitor PD331618

• PDB DOI: https://doi.org/10.2210/pdb3BIZ/pdb

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


• Deposited: 2007-12-02 Released: 2007-12-25 
• Deposition Author(s): Squire, C.J., Dickson, J.M., Ivanovic, I., Baker, E.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.247 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 

Starting Model: experimental

Literature

Synthesis and structure-activity relationships of soluble 8-substituted 4-(2-chlorophenyl)-9-hydroxypyrrolo[3,4-c]carbazole-1,3(2H,6H)-diones as inhibitors of the Wee1 and Chk1 checkpoint kinases.

Smaill, J.B., Lee, H.H., Palmer, B.D., Thompson, A.M., Squire, C.J., Baker, E.N., Booth, R.J., Kraker, A., Hook, K., Denny, W.A.

(2008) Bioorg Med Chem Lett 18: 929-933

• PubMed: 18191399 
• DOI: https://doi.org/10.1016/j.bmcl.2007.12.046
• Primary Citation of Related Structures:  
  3BI6, 3BIZ


• PubMed Abstract: 
  

  Pyrrolo[3,4-c]carbazoles bearing solubilising basic side chains at the 8-position retain potent Wee1 and Chk1 inhibitory properties in isolated enzyme assays, and evidence of G2/M checkpoint abrogation in several cellular assays. Co-crystal structure studies confirm that the primary binding to the Wee1 enzyme is as described previously, with the C-8 side chains residing in an area of bulk tolerance.

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Organizational Affiliation: 

Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.81 kDa 
• Atom Count: 2,153 
• Modelled Residue Count: 250 
• Deposited Residue Count: 287 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Wee1-like protein kinase	A	287	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
61E	C [auth A]	4-(2-chlorophenyl)-8-[3-(dimethylamino)propoxy]-9-hydroxy-6-methylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-dione C26 H24 Cl N3 O4 ZWRDUCSPTGMSHB-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
61E	BindingDB:  3BIZ	IC50: 58 (nM) from 1 assay(s)
	PDBBind:  3BIZ	IC50: 58 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.247 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.859	α = 90
b = 68.859	β = 90
c = 156.238	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-25 
Deposition Author(s): Squire, C.J., Dickson, J.M., Ivanovic, I., Baker, E.N.

Revision History  

• Version 1.0: 2007-12-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description