2R0U

Crystal Structure of Chek1 in Complex with Inhibitor 54

• PDB DOI:  https://doi.org/10.2210/pdb2R0U/pdb

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


• Deposited: 2007-08-21 Released: 2007-10-30 
• Deposition Author(s): Yan, Y., Ikuta, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.218 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

Synthesis and evaluation of substituted benzoisoquinolinones as potent inhibitors of Chk1 kinase.

Garbaccio, R.M., Huang, S., Tasber, E.S., Fraley, M.E., Yan, Y., Munshi, S., Ikuta, M., Kuo, L., Kreatsoulas, C., Stirdivant, S., Drakas, B., Rickert, K., Walsh, E.S., Hamilton, K.A., Buser, C.A., Hardwick, J., Mao, X., Beck, S.C., Abrams, M.T., Tao, W., Lobell, R., Sepp-Lorenzino, L., Hartman, G.D.

(2007) Bioorg Med Chem Lett 17: 6280-6285

• PubMed: 17900896 
• DOI: https://doi.org/10.1016/j.bmcl.2007.09.007
• Primary Citation of Related Structures:  
  2R0U


• PubMed Abstract: 
  

  From HTS lead 1, a novel benzoisoquinolinone class of ATP-competitive Chk1 inhibitors was devised and synthesized via a photochemical route. Using X-ray crystallography as a guide, potency was rapidly enhanced through the installation of a tethered basic amine designed to interact with an acidic residue (Glu91) in the enzyme pocket. Further SAR was explored at the solvent front and near to the H1 pocket and resulted in the discovery of low MW, sub-nanomolar inhibitors of Chk1.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 37.33 kDa 
• Atom Count: 2,471 
• Modelled Residue Count: 269 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Chk1	A	323	Homo sapiens	Mutation(s): 0  Gene Names: CHEK1, CHK1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14757 (Homo sapiens) Explore O14757  Go to UniProtKB:  O14757
PHAROS:  O14757

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M54	B [auth A]	6-(3-aminopropyl)-4-(3-hydroxyphenyl)-9-(1H-pyrazol-4-yl)benzo[h]isoquinolin-1(2H)-one C25 H22 N4 O2 BUSJQQYKXHYDNN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
M54	BindingDB:  2R0U	IC50: 1 (nM) from 1 assay(s)
	PDBBind:  2R0U	IC50: 1 (nM) from 1 assay(s)
	Binding MOAD:  2R0U	IC50: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.218 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.26	α = 90
b = 65.54	β = 94.27
c = 58.5	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
Deposition Author(s): Yan, Y., Ikuta, M.

Revision History  

• Version 1.0: 2007-10-30
  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