2IO6 | pdb_00002io6

Wee1 kinase complexed with inhibitor PD330961


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.273 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 330Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Synthesis and structure-activity relationships of N-6 substituted analogues of 9-hydroxy-4-phenylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-diones as inhibitors of Wee1 and Chk1 checkpoint kinases.

Smaill, J.B.Baker, E.N.Booth, R.J.Bridges, A.J.Dickson, J.M.Dobrusin, E.M.Ivanovic, I.Kraker, A.J.Lee, H.H.Lunney, E.A.Ortwine, D.F.Palmer, B.D.Quin, J.Squire, C.J.Thompson, A.M.Denny, W.A.

(2008) Eur J Med Chem 43: 1276-1296

  • DOI: https://doi.org/10.1016/j.ejmech.2007.07.016
  • Primary Citation of Related Structures:  
    2IN6, 2IO6

  • PubMed Abstract: 

    A series of N-6 substituted 9-hydroxy-4-phenylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-diones were prepared from N-substituted (5-methoxyphenyl)ethenylindoles. The target compounds were tested for their ability to inhibit the G2/M cell cycle checkpoint kinases, Wee1 and Chk1. Analogues with neutral or cationic N-6 side chains were potent dual inhibitors. Acidic side chains provided potent (average IC(50) 0.057 microM) and selective (average ratio 223-fold) Wee1 inhibition. Co-crystal structures of inhibitors bound to Wee1 show that the pyrrolo[3,4-c]carbazole scaffold binds in the ATP-binding site, with N-6 substituents involved in H-bonding to conserved water molecules. HT-29 cells treated with doxorubicin and then target compounds demonstrate an active Cdc2/cyclin B complex, inhibition of the doxorubicin-induced phosphorylation of tyrosine 15 of Cdc2 and abrogation of the G2 checkpoint.


  • Organizational Affiliation

    Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 1020, New Zealand. j.smaill@auckland.ac.nz


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Wee1-like protein kinase287Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30291
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
330
Query on 330

Download Ideal Coordinates CCD File 
B [auth A]9-HYDROXY-6-(3-HYDROXYPROPYL)-4-(2-METHOXYPHENYL)PYRROLO[3,4-C]CARBAZOLE-1,3(2H,6H)-DIONE
C24 H20 N2 O5
AOGOZJCRIFBTTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
330 BindingDB:  2IO6 IC50: 30 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.925α = 90
b = 69.925β = 90
c = 157.92γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 330Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description