5V5Y

CRYSTAL STRUCTURE OF HUMAN WEE1 KINASE DOMAIN IN COMPLEX WITH MK1775


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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1021/acs.jmedchem.7b00996
  • Primary Citation of Related Structures:  
    5V5Y, 5VC3, 5VC5, 5VC4, 5VC6, 5VCZ, 5VD3, 5VCW, 5VCV, 5VCY

  • 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). Purifie ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Wee1-like protein kinaseA289Homo sapiensMutation(s): 0 
Gene Names: WEE1
EC: 2.7.10.2
Find proteins for P30291 (Homo sapiens)
Explore P30291 
Go to UniProtKB:  P30291
NIH Common Fund Data Resources
PHAROS  P30291
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8X7
Query on 8X7

Download CCD File 
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
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8X7Kd:  13.399999618530273   nM  Binding MOAD
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 = 50.08α = 90
b = 63.1β = 90
c = 82.46γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United StatesU01 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