Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 33.22 kDa 
• Atom Count: 2226 
• Modelled Residue Count: 259 
• Deposited Residue Count: 289 
• Unique protein chains: 1

5V5Y

CRYSTAL STRUCTURE OF HUMAN WEE1 KINASE DOMAIN IN COMPLEX WITH MK1775

• PDB DOI: 10.2210/pdb5V5Y/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-03-15 Released: 2017-08-23 
• Deposition Author(s): ZHU, J.-Y., SCHONBRUNN, E.
• Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.215 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 

Literature

Structural Basis of Wee Kinases Functionality and Inactivation by Diverse Small Molecule Inhibitors.

Zhu, J.Y., Cuellar, R.A., Berndt, N., Lee, H.E., Olesen, S.H., Martin, M.P., Jensen, J.T., Georg, G.I., Schonbrunn, E.

(2017) J Med Chem 60: 7863-7875

• PubMed: 28792760 
• DOI: 10.1021/acs.jmedchem.7b00996
• Primary Citation of Related Structures:  
  5V5Y, 5VC3, 5VC4, 5VC5, 5VC6, 5VCV, 5VCW, 5VCX, 5VCY, 5VCZ, 5VD0, 5VD1, 5VD2, 5VD3, 5VDK


• PubMed Abstract: 
  

Members of the Wee family of kinases negatively regulate the cell cycle via phosphorylation of CDK1 and are considered potential drug targets. Herein, we investigated the structure-function relationship of human Wee1, Wee2, and Myt1 (PKMYT1). Purified recombinant full-length proteins and kinase domain constructs differed substantially in phosphorylation states and catalytic competency, suggesting complex mechanisms of activation. A series of crystal structures reveal unique features that distinguish Wee1 and Wee2 from Myt1 and establish the structural basis of differential inhibition by the widely used Wee1 inhibitor MK-1775. Kinome profiling and cellular studies demonstrate that, in addition to Wee1 and Wee2, MK-1775 is an equally potent inhibitor of the polo-like kinase PLK1. Several previously unrecognized inhibitors of Wee kinases were discovered and characterized. Combined, the data provide a comprehensive view on the catalytic and structural properties of Wee kinases and a framework for the rational design of novel inhibitors thereof.

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Organizational Affiliation: 

Drug Discovery Department, Moffitt Cancer Center , Tampa, Florida 33612, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Wee1-like protein kinase	A	289	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8X7	B [auth A]	1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one C27 H32 N8 O2 BKWJAKQVGHWELA-UHFFFAOYSA-N
DMS	C [auth A], D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
8X7	Binding MOAD:  5V5Y	Kd: 13.4 (nM) from 1 assay(s)
	BindingDB:  5V5Y	Kd: min: 3.2, max: 13 (nM) from 2 assay(s)
		IC50: min: 1, max: 10 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.215 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.08	α = 90
b = 63.1	β = 90
c = 82.46	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-03-15 
• Released Date: 2017-08-23 
Deposition Author(s): ZHU, J.-Y., SCHONBRUNN, E.

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Funding Organization	Location	Grant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	U01 HD076542

Revision History  

• Version 1.0: 2017-08-23
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Database references, Refinement description
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence