2YM8

Crystal structure of checkpoint kinase 1 (Chk1) in complex with inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-Guided Evolution of Potent and Selective Chk1 Inhibitors Through Scaffold Morphing.

Reader, J.C.Matthews, T.P.Klair, S.Cheung, K.M.J.Scanlon, J.Proisy, N.Addison, G.Ellard, J.Piton, N.Taylor, S.Cherry, M.Fisher, M.Boxall, K.Burns, S.Walton, M.I.Westwood, I.M.Hayes, A.Eve, P.Valenti, M.De Haven Brandon, A.Box, G.Van Montfort, R.L.M.Williams, D.H.Aherne, G.W.Raynaud, F.I.Eccles, S.A.Garrett, M.D.Collins, I.

(2011) J Med Chem 54: 8328

  • DOI: 10.1021/jm2007326
  • Primary Citation of Related Structures:  
    2YM6, 2YM7, 2YM8, 2YM3, 2YM4, 2YM5

  • PubMed Abstract: 
  • Pyrazolopyridine inhibitors with low micromolar potency for CHK1 and good selectivity against CHK2 were previously identified by fragment-based screening. The optimization of the pyrazolopyridines to a series of potent and CHK1-selective isoquinoline ...

    Pyrazolopyridine inhibitors with low micromolar potency for CHK1 and good selectivity against CHK2 were previously identified by fragment-based screening. The optimization of the pyrazolopyridines to a series of potent and CHK1-selective isoquinolines demonstrates how fragment-growing and scaffold morphing strategies arising from a structure-based understanding of CHK1 inhibitor binding can be combined to successfully progress fragment-derived hit matter to compounds with activity in vivo. The challenges of improving CHK1 potency and selectivity, addressing synthetic tractability, and achieving novelty in the crowded kinase inhibitor chemical space were tackled by multiple scaffold morphing steps, which progressed through tricyclic pyrimido[2,3-b]azaindoles to N-(pyrazin-2-yl)pyrimidin-4-amines and ultimately to imidazo[4,5-c]pyridines and isoquinolines. A potent and highly selective isoquinoline CHK1 inhibitor (SAR-020106) was identified, which potentiated the efficacies of irinotecan and gemcitabine in SW620 human colon carcinoma xenografts in nude mice.


    Related Citations: 
    • Identification of Inhibitors of Checkpoint Kinase 1 Through Template Screening.
      Matthews, T.P., Klair, S., Burns, S., Boxall, K., Cherry, M., Fisher, M., Westwood, I.M., Walton, M.I., Mchardy, T., Cheung, K.J., Van Montfort, R., Williams, D., Aherne, G.W., Garrett, M.D., Reader, J., Collins, I.
      (2009) J Med Chem 52: 4810
    • Design and Evaluation of 3,6-Di(Hetero)Aryl Imidazo[1,2-A]Pyrazines as Inhibitors of Checkpoint and Other Kinases.
      Matthews, T.P., Mchardy, T., Klair, S., Boxall, K., Fisher, M., Cherry, M., Allen, C.E., Addison, G.J., Ellard, J., Aherne, G.W., Westwood, I.M., Van Montfort, R., Garrett, M.D., Reader, J.C., Collins, I.
      (2010) Bioorg Med Chem Lett 20: 4045

    Organizational Affiliation

    Cancer Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE CHK1A289Homo sapiensMutation(s): 0 
Gene Names: CHEK1CHK1
EC: 2.7.11.1
Find proteins for O14757 (Homo sapiens)
Explore O14757 
Go to UniProtKB:  O14757
NIH Common Fund Data Resources
PHAROS  O14757
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YM8
Query on YM8

Download CCD File 
A
(R)-5-(8-CHLOROISOQUINOLIN-3-YLAMINO)-3-(1-(DIMETHYLAMINO)PROPAN-2-YLOXY)PYRAZINE-2-CARBONITRILE
C19 H19 Cl N6 O
SRBJWIBAMIKCMV-GFCCVEGCSA-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 %)
YM8IC50:  13   nM  Binding MOAD
YM8IC50 :  13   nM  PDBBind
YM8IC50:  13   nM  BindingDB
YM8IC50:  55   nM  BindingDB
YM8IC50:  6.099999904632568   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.77α = 90
b = 65.47β = 95.38
c = 57.93γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2012-01-11
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Data collection