Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.98 kDa 
• Atom Count: 2198 
• Residue Count: 246 
• Unique protein chains: 1

2YM8

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

• DOI: 10.2210/pdb2YM8/pdb

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


• Deposited: 2011-06-06 Released: 2012-01-11 
• Deposition Author(s): 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., Brandon, A.H., Box, G., vanMontfort, R.L.M., Williams, D.H., Aherne, G.W., Raynaud, F.I., Eccles, S.A., Garrett, M.D., Collins, I.

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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 

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

• PubMed: 22111927 
• 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 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.

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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

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE CHK1	A	289	Homo sapiens	Mutation(s): 0  Gene Names: CHEK1, CHK1 EC: 2.7.11.1
Find proteins for O14757 (Homo sapiens) Explore O14757  Go to UniProtKB:  O14757
NIH Common Fund Data Resources
PHAROS:  O14757 GTEx:  ENSG00000149554

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YM8	A	(R)-5-(8-CHLOROISOQUINOLIN-3-YLAMINO)-3-(1-(DIMETHYLAMINO)PROPAN-2-YLOXY)PYRAZINE-2-CARBONITRILE C19 H19 Cl N6 O SRBJWIBAMIKCMV-GFCCVEGCSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
YM8	IC50:  13   nM  Binding MOAD
YM8	IC50 :  13   nM  PDBBind
YM8	IC50:  13   nM  BindingDB
YM8	IC50:  55   nM  BindingDB
YM8	IC50:  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 = 44.77	α = 90
b = 65.47	β = 95.38
c = 57.93	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-06-06 
• Released Date: 2012-01-11 
Deposition Author(s): 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., Brandon, A.H., Box, G., vanMontfort, R.L.M., Williams, D.H., Aherne, G.W., Raynaud, F.I., Eccles, S.A., Garrett, M.D., Collins, I.

Revision History 

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