2HOG

crystal structure of Chek1 in complex with inhibitor 20

• PDB DOI:  https://doi.org/10.2210/pdb2HOG/pdb

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


• Deposited: 2006-07-14 Released: 2007-04-24 
• 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: 0.236 
• R-Value Work: 0.204 

Literature

3-(Indol-2-yl)indazoles as Chek1 kinase inhibitors: Optimization of potency and selectivity via substitution at C6.

Fraley, M.E., Steen, J.T., Brnardic, E.J., Arrington, K.L., Spencer, K.L., Hanney, B.A., Kim, Y., Hartman, G.D., Stirdivant, S.M., Drakas, B.A., Rickert, K., Walsh, E.S., Hamilton, K., Buser, C.A., Hardwick, J., Tao, W., Beck, S.C., Mao, X., Lobell, R.B., Sepp-Lorenzino, L., Yan, Y., Ikuta, M., Munshi, S.K., Kuo, L.C., Kreatsoulas, C.

(2006) Bioorg Med Chem Lett 16: 6049-6053

• PubMed: 16978863 
• DOI: https://doi.org/10.1016/j.bmcl.2006.08.118
• Primary Citation of Related Structures:  
  2HOG


• PubMed Abstract: 
  

The development of 3-(indol-2-yl)indazoles as inhibitors of Chek1 kinase is described. Introduction of amides and heteroaryl groups at the C6 position of the indazole ring system provided sufficient Chek1 potency and selectivity over Cdk7 to permit escape from DNA damage-induced arrest in a cellular assay. Enzyme potency against Chek1 was optimized by the incorporation of a hydroxymethyl triazole moiety in compound 21 (Chek1 IC(50)=0.30nM) that was shown by X-ray crystallography to displace one of three highly conserved water molecules in the HI region of the ATP-binding cleft.

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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.

Macromolecule Content

• Total Structure Weight: 37.22 kDa 
• Atom Count: 2,464 
• Modelled Residue Count: 272 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Chk1	A	322	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
710	B [auth A]	(5-{3-[5-(PIPERIDIN-1-YLMETHYL)-1H-INDOL-2-YL]-1H-INDAZOL-6-YL}-2H-1,2,3-TRIAZOL-4-YL)METHANOL C24 H25 N7 O FNWHPLLNMLOZTL-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
710	Binding MOAD:  2HOG	IC50: 0.3 (nM) from 1 assay(s)
	PDBBind:  2HOG	IC50: 0.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.236 
• R-Value Work: 0.204 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.97	α = 90
b = 65.53	β = 94.2
c = 58.4	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-24 
Deposition Author(s): Yan, Y., Ikuta, M.

Revision History  

• Version 1.0: 2007-04-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description